I imagine that the first Star Trek OFU(which, as I have found out, is called OFUST: DS9. What a mouthful. Seriously, try saying it all at once.) was devastated by its Designated OFU Emergency, and the mini-Tribbles have multiplied until they have the run of the place. Either that, or it survived perfectly well and just doesn't want to make contact with the OFAS for administrative purposes. That second option isn't as interesting, though.

So, the new mini type is Q's doing, just like the abandoned planet with HQ-styled halls is Q's doing and the numerous canons plucked from all across time-space and given indefinite leave from their duties is Q's doing? That's the great thing about Q. He is to Star Trek what the Unicron Singularity is to Transformers, or the events of Thief of Time are to the Discworld, except instead of being limited to only space and time(at which point the term "limited" has already come into question), the unexplainable things could come from anywhere. Dealing with inconsistency or general confusion in Star Trek can be easily explained by saying "This is the home continuum of a capricious omnipotent being with free rein over the cosmos. The question isn't whether it can be done, the question is why something like it hadn't been done before."

If the Borg's name-mistakes had all been linked into one central Collective, the mini-Queens would probably just serve as coordinators of some sort. As much as I like the idea of a Borg Queen power struggle acted out by mini-Gorn, it's not really a Borg thing to do to squabble within their ranks when there is a task to be done. In this case, it would be defense of the Academy and the sanctity of the Collective rather than assimilation of the other minis(probably), but it would be taken up with no less fervor.

Speaking of the mini-Colossi, is there a Board-run adoption center for their continuum, like there is for the mini-Balrogs? One of my agents-in-progress has a soft spot for mechanical minis, and while I don't know much about Mass Effect other than the basics of the races and setting, and thus couldn't spork a story myself, he'd probably enjoy having a little geth running around the RC. Between your and Herr Wozzeck's missions alone, there should be at least twenty of the little guys without supervisors.
I almost said "owners", and then I remembered what typical mini behavior is like.