While I agree that we should probably just wait and see, I'm ALSO going to exercise my prerogative of blatant hypocrisy and say that I'd expect it to be easier to recruit, fund, and organize non-Imperial magic users if the research institute is built under K8P's authority rather than under the Empire's. I will note that I'm saying "easier," because it would probably still be possible to work out some loophole-based way to work with non-Imperial magic users (I'm going to abbreviate that to NIMUs now).
But, every proposal I've heard to make that fly under the Articles sounds like it would entail setting up multiple legally distinct research entities (a minimum of two, one for College mages and one for NIMUs). This creates multiple problems. One, any entity directly employing NIMUs cannot be funded by the Deeds. If we have to fund that out of pocket, it will get extremely expensive extremely quickly. Finding data on how much you're expected to pay wizards etc. is a pain and a half; the only number I could find from WFRP 2e was that a Wizard Lord's expected pay per year was 300-800 gold. If we take that as our referent, then if we wanted anybody of a roughly equivalent rank to us to be involved, we could afford very few of them and not for very long. If we assume an equivalent to a "regular" Magister is, idk, half that, it still adds up very quickly, and that's independent of any costs for providing research materials and etc. that we might be expected to cover. Two, anything that isn't being officially part of whatever institute was formally legitimated by the Empire or K8P would presumably be accordingly less prestigious. This would make it harder to attract good candidates, and whoever's willing would probably want more money as well to compensate for the less impressive item on their resume. Three, have you ever taken a look at the bureaucracy for one college? Do you really want to organize multiple such bureaucracies with the intent to have them operate in tandem? That's just asking for trouble IMO. And if we hire the NIMUs without setting up a specific legal framework/institution to do the hiring - as "independent consultants" or whatever - that raises the question of who exactly is doing the hiring. It can't be us in our capacity as a Magister of the Empire, because that would, again, fall in violation of the Articles. If we hired them as K8P's Loremaster that might work, but AFAICT the plan is we'll probably leave that role to focus more heavily on Waystones. It just... gets messy, one way or another.
So the tl;dr is that what I expect to get out of a Boon research center that we can't get out of a Deed research center is "making everything that isn't hiring and working with exclusively Collegiate mages easier, cheaper, and less complicated".