In the case of someone outside the building listening in, Obfuscation applies - as that is literally what Obfuscation is designed to do. In the case of someone casting their senses into the building, the rune of Fogginess should hamper their perceptions.
Like from my perspective the argument is trying to argue for two contradictory things at once, and is therefore unconvincing.
However, we have an easy source of clarification. @soulcake does Snorri think he has any runes that could hamper scrying or similar magic?
Back to the topic at hand I think that in the case of the anti-scrying runes, they invented them for power. Specificity in runes generates more powerful effects as a trend. See Piercing Sight from Snerra as another example.
From that thought I take the conclusion that we are not without scrying defenses at all. Simply more powerful specific ones, like the difference between a Spelleating and Spellturning rune. The main points you need to convince me on are their necessity (I am somewhat convinced here), and their urgency - that we can't put them in a small statue or carried items. And like, for that second one, we already know we can (albeit) slowly change the Services of Khazagar: taking some time to work up Wardstones as statues or carried items, seems entirely workable to add in and is far less arduous than changing an entire Service.
When they were initially created we already know they weren't used as Structural Static Runes, but instead as movable Talismanic or Banner runes. And it makes the most sense to me to use them in the use case they were designed for.
From my perspective, Obfuscation proves my point. Just as you need Obfuscation to fill one gap that Fogginess has, so we need the wardstones' rune to block scrying. They're different gaps in the defences that need to be filled.
My argument is that runes do what they're designed to do. They're not conceptual, except for Ancestor Runes, which these aren't. None of the runes you cite were developed by runesmiths to block scrying. They're designed to block physical intrusion and physical eavesdropping. The runesmiths who made them may not even have been aware that scrying was possible, as it's not a thing that previous enemies of the dwarves really had much access to, not being part of the normal repertoire of beastmen, even their shaman. The prophets of Hashut and Fimir sorcerers do.
Remember, up until the very end of the pre-Vortex period we weren't fighting daemon armies, so not even then would there have been the time or need to develop anti-scrying runes. Also, with the way chaos armies work, scrying would have made less of a difference,
Basically, if I'm right, we're leaving a small but very serious flaw in our defences that compromises the very purpose of the institution. If Thungni comes and takes a look and judges it inadequate because it's at risk of leaking secrets to magical scrying, trying to make an excuse that we were planning to patch the vulnerability at some undefined time later while leaving the security hole open until then is unlikely to satisfy him. And yes, this is a bit of a worst case scenario, but he's just told us that he'd going to be making a judgement on our results here. Him coming and taking a look at what precautions we think are most important and so built in from the start would be completely reasonable.
I think Thungni would be much more impressed that we have built in defence in depth against information leakage from scrying from the start, than say, preparations for an even more over the top figurehead gronti,
One is plugging a basic potential security hole to sensors compliance with the strictures around the secrecy of runelore that could be exploited from day one, the other is just reinforcing physical defences which weare already so incredibly strong there's no real prospect of them being defeated for centuries, in which time we will be further improving those defences.
As I say, the real danger of what we're trying here isn't physical conquest by an army the gronti can fight, it's espionage performed by enemy mages. Even if the place wa conquered there's almost certainly be time for failsafe self-destruct mechanisms to destroy any records that gave hints about runelore. Vulnerability to scrying is a persistent threat that we might not even notice if we fall victim to. And it's one that we need to make as strong as possible from the start. If we leave gaps or weaknesses then gradually improve it our enemies can try to develop their own capabilties based on what we know. Much better to put up a strong defence from the start.
Almost lastly, without examining the Wardstones and what they do that the other privacy runes don't, how would we know IC whether the current runes are sufficient to justify us being told OOC? The only indication we have is that Snorri knowing those runes didn't make the project redundant, or reduce the actions required for the project, and that existing privacy runes were inadequate to defend against the leakage of runelore in Dum, or to protect the surviving loyalists. In this, we should err on the side of caution, not just assume that existing defences that we have examples of not working will be certain to work here and the prior example was a special case.
And lastly, we have a special benefit from Valaya's insight for completing the Wardstone project, so we should expect that we'll get a particularly good result here. Generally, warding the runiversity should be one of the highest priorities, to justify why it's not an irresponsible thing to do. Getting a special bonus to warding things seems like a good way to do that, as it may spill over to better warding runes more generally if we're fortunate.
In addition to the Rune of Kingship, one argument for Mind of Things is that it opens the possibility of Holocorns far more secure than any book can ever be. But we aren't likely to get to that before Mobile Deep Magic, so I will rather invest heavily into Movement of Things for Deep Magic, which is far more likely to gain swift acceptance than Holocorns.
We also know that radical things that are built into the institution from the start are much more likely to gain acceptance than later additions.
Deep magic powered runes aren't at all radical, so aren't urgent.