I am not sure if you have the correct expectation. Waystones are not some kind of superweapon. They are infrastructure. Lots of upfront cost in exchange for a passive longterm benefit. The reasearch fortunately has two long-lived species as eager customers, but we the readers will likely only actually see tangible results in a timeskip after Mathilde either dies or gets retired from the position of protagonist.
A large part of the problem with Waystones is that beyond the High Elves (and maybe the Lizardmen but they do their own thing) nobody else really pokes at them. The Dawi use them but only as ancient infrastructure that barely anyone knows exists, the Colleges don't really make active efforts to study them, the Eonir don't have a large geographical area so their portion of the Waystone network is bound to be really small.
Changing that would be pretty transformative - the Dawi lost a Karak to the Warp because they don't really understand the Waystone thing. Thorgrim basically put the Karaz Ankor into Slayer mode because he didn't understand the Waystone thing. The Empire is routing all their magic to Ulthuan because nobody really understands the Waystone thing.
Waystones are important and juicy research - and I say that even though I sort of favour Bodyguard a tiny bit more at the moment.
You are overestimating Mathilde's degree of autonomy, I think.
We will be enacting Heidi's ambition and agenda. She may not be strictly speaking ordering Mathilde about, but that's more of just ordering about not being her style.
Remember that Heidi is one of very few people better than Mathilde at intrigue, probably, and definitely better at the specifically court intrigue. Mathilde will certainly have ample space for (title drop!) divided loyalties and whether to do what Heidi asks, but that's not really the same as working "with", it's still working "for", just with room to double-cross and backstab Heidi if we have to.
Mathilde is a Grey Lady Magister. A fantastically well connected and influential Grey Lady Magister even.
She's got the autonomy because Heidi has very little to hang over Mathilde's head. Heidi would have to be monumentally stupid to give us a reason to 'rebel' - not only would she going against one of the deadliest assassin-mages in the Old World; who also happens to be a political powerhouse but she'd also do it with Ranald in our corner and not hers.
Will Heidi try to manipulate and do tricky stuff? Yes... but then how else are we going to level up that Intrigue?
Frankly a lot of the appeal of Bodyguard, Waystone and Loremaster is that they work in the stuff we're good at - Intrigue (and maybe a bit of Piety) for the first; Learning for the second and third.
The reason why I don't like Markgraf is that it doesn't really focus on what Mathilde is good at. It doesn't help us be a better mage, doesn't really help us be a better Ranald-ite and doesn't even particularly help us at intrigue.
It moderately helps at a Martial oriented path... but a lot of it is going to be Stewardship with some Diplomacy sprinkled in.