I think when looking at "Who might be motivated to disrupt a Logistics/Infrastructure Project?", you have to look at ways to entangle this "Boring But Practical" Chaos-goal, with some other Prestige-gaining-goal or Personal-vengeance-goal.
i.e. The best way to get somebody to work against the Waystone Project, is to pick somebody who has cause to want to see Laurelorn, Middenland, or Karak Eight Peaks, taken down a peg. Or they have grudges with individual members of the Project involved; rivals of Hatalath or Niedzwenka or Mathilde or whatever. In which case, foiling the Waystone Project or discrediting the participants of it -- whether the nations or the individuals involved -- would be a method to achieve the real thing the Chaos patsy wants; personal satisfaction, the lessening of a rival polity's prestige, or the elimination of a threat to their personal or group prestige or wealth or something.
Like somebody from Marienburg or Nordland maybe.
You know how people have mentioned that it didn't feel like there was a "main villain" opposing us? Well, that's because even when there was a villain -- the Countess Von Carsten, and Alkharad -- they didn't always enter the narrative stage in a theatrically-appropriate way which easily raised heat. Alkharad was introduced doing an assassination attempt on Roswita, and we dramatically foiled it; then we learned more about him in the next update, and resolved to hunt him down; we then investigated him (and several other vampire locations too I think, briefly?) in the next turn or so; and then we went and assassinated him. 3 "turns" total of being an arch-nemesis to Mathilde; introduced in an interlude/campaign turn; investigated in a main-turn; investigated and assassinated in another main turn. ((I forget if we observed his mist projection on the same turn we assassinated him... I don't think we did. I think those were two separate turns.))
And yet, Alkharad was a significant nemesis to Stirland in his backstory which Mathilde did not interact with until she stumbled upon him at the end of his "story". He was tearing through Roswita's greatswords; he was launching constant assassination attempts. He was training up an entire Necromancy college. He was a severe threat and antagonist, and could have been a major or moderate Warhammer novel or RPG adventure villain for the entire province. Even as-is, he was a threat to the province, one of many if probably the most organized one. It's just... we ended him. And then all the rest of the Vampires kind of crumpled in the face of Stirland's army and the Battle Mages.
Countess Von Carstein we never met or talked to at all. Did anybody ever even retrieve her Vampire Skull from where it was? Did we confirm her death? Eh. Whatever. She's dead. A lot of what was going wrong in Stirland and Sylvania was her doing; but we spent a lot of time rooting out corruption and turncoats in Stirlanders, and a lot of organizing. While Van Hal was Preparing(TM). So while we faced off against her at the end of a chessboard... it was a bit impersonal in some way. We just happened to play Civ/CK better than she did, and play Total War better than she did.
That's not even to mention how many "main villains" of Karak Eight Peaks got swatted by the Throng, or by one of the rival enemy armies, or whatnot.
Even aside from obvious-name-recognition ones like Skarsnik or Sleek Sharpwit... how many characters in Karak Eight Peaks had -- or were -- the potential to be Arch-Nemesises of Mathilde or Belegar? There was a Goblin Warchief making deals with Moulder; we Accidentaly'd him. Well. It was intentional, we just didn't know we killed somebody really important. There was probably a leader of Moulder present too, who could have had impressive chops. There were the Eshin Skaven. Hell, remember that one 1d6 roll for "Who is the Eshin Sorcerer betraying" we got? The 1 on that d6 would have been a fucking Verminlord.
It would have been a sudden antagonist, and a very horrifying fight -- if we had made it a fight at all, rather than deciding "Screw this, I'm getting the army/telling the Ice Dragon/using Clan Mors to kill this guy!"
The problem is it would have been sudden... It's hard to write a novel-worthy longrunning antagonist that your protagonist faces off with, again and again, in the type of game that this quest runs.
Who was the guy behind the Skull River Ambush? He managed to have intel on when the Okral were going to leave -- something easily enough achievable if you have some informant in Eight Peaks, just somebody who sends a letter or news to somebody else going "Wow, the Dwarfs from Karaz-A-Karak are leaving!" without even knowing much more than that, even if it looks really hard for somebody who's not in Karak Eight Peaks to learn -- and prepare an explosive for them.
We never tracked him down. We never even spent much thought on him, other than desperately but busily hoping that this doesn't cause 8 Peaks or KAK to aggro on Marienburg and/or Ulthuan to retort, while we busied ourselves with Karag Dum. We just... sort of moved on from him. Does that make him a bad antagonist? Was he supposed to do other stuff to us? What if he did and we just didn't notice that stuff? We didn't notice him putting up whatever intelligence infrastructure that allowed him to know when the Okral were intending to leave, after all! What if he also took several other potshots to us, like being behind the Blackwater Canal disruption?
Did he fail miserably, and then get rolled up by Marienburg in their purge? Or did he succeed? Was he a Nurglite or Tzeentch worshipper who pivoted from "Disrupt the Karaz Ankor" to "Destroy my Slaaneshi pleasure cult rivals"?
Algard did say that fights between the 6-cult of the Soulflayer and the 9-cult of the Eldritch Watcher had erupted in the Empire -- perhaps Marienburg was another such fight, wherein the Eldritch Watcher's cultist outmaneuvered the Soulflayer's cultist?
If he is extant in Marienburg, how would we go about detecting that? How would we, an Imperial Shadow Wizard, do skullduggery in Marienburg? Marienburg wouldn't want an Imperial butting in. It wouldn't want a Shadow Wizard doing so. It wouldn't want Literally The Head Of The EIC and friend to Laurelorn/Middenland/Karak Eight Peaks doing so either. We could still do so. We could even do so as an official Imperial ambassador or whatever. Just... Would be hard. Or we could do so surreptitiously; we're good at that, and we have the Deceiver and Night Prowler coin facets. We could sneak in. How would we gather information though?
If there is a cultist left in Marienburg, and is even more successful in his lord's esteem, what might he pull off in the future? What if he assassinates Teclis (or Tyrion, or some important functionary or ambassador of the Phoenix King) who comes to Marienburg on their way to fight the Everchosen in the north?
If we suddenly found out that Teclis had died in Marienburg as we were gearing up to fight the Everchosen, would that feel "cheap" and sudden to us? I mean, it's not that necessarily every misfortune or enemy action that occurs in the future, has to be coming from an enemy NPC that was spawned at the start or midway through the quest which Mathilde could plausibly have pursued or managed to catch wind of and then theoretically taken care of like it was an MMO quest or forum quest; it's entirely possible for Boney to roll dice for cultist or Norscan activity and interference and success levels when plotting the Everchosen's war campaign, and to declare that Phoenix King Finubar's personal ship got sunk by a mercenary Dawi Zharr sub or something. That would feel cheap and sudden, but it could happen. It could happen as a result of a Quest-original enemy NPC from the start or middle of the game that was never encountered and wound up doing their stuff on the other end of the continent from us up until his activities suddenly intersected with us again; or it could happen as a result of a general series of rolls of "How well does Chaos do? And how do I justify or explain this action?" that would be reasonable or expected to make as a general world-building thing. Hell, maybe it would be a Malekith or Morathi plot rather than a Chaos plot; some way to spike Ulthuan's influence in the Old World, piss off Ulthuan at Marienburg or whomever was nearby, or just cause decision paralysis in Ulthuan as they rushed to deal with their own problems. Maybe it'd be a Druchii plot from the guys dealing with the Eonir, who had found no success in Laurelorn but went for a longshot; or maybe the reverse. Maybe if the Druchii were successful with getting some ins and trade with the Eonir, this resulted in them being able to set up a spy ring that reached through the Empire or into Marienburg, and so knew how to hit an important Ulthuani visitor.
All these things could happen, and we might never know, or we might blame ourselves for not "obviously" dealing with or heading off this or that problem. But, like... Enemies setting up spy rings in the huge ass territory of the Empire or the Old World is just a thing that happens. The use of merchants and mercantile connections to spy or smuggle stuff is just a thing that happens. ((Which can be one reason that nations might frownyface at foreign merchants. Or any easily subverted or infiltrated enterprise. But at the same time, they might like to do their own subversion and spying, for the exact same reasons, so...)) That's just life. That's just life in progress. At some point, you have to accept that you can't preemptively snuff out every problem, and that you have to rely on bodyguards and armies and stuff, and having a quick sword hand or trigger finger. That you have to rely on the things you did do right and the preparations you made -- armies, supply routes, friendly foreign diplomatic contacts, spy rings of your own, bodyguards, personal training -- to fight off the entropy and enemy action of all the other active actors in the rest of the world.