Well a big part of Fanime Tournaments and the Gaming room in general is the spectacle for the attendees to watch, no? Moving the PCs to a smaller room would mean less people can be in the room at one time, and of course the room is going to be a oven. I mean they could project the match someone to the main room I guess, but that is some unneeded complication.
Also last I checked they did not use dedicated PCs for the tournament, they were also used for general PC Gaming as well. They all need to be in the gaming hall.
As for splitting random teams and premade teams, at what point does one face the other, and at that point, besides the random team maybe having a chance to play more then one round or two, does the end result change?
The only way I can see it being fair to split those teams is to do a total split into two separate tournaments, that way one never faces the other and everything can be 'fair'. I dont think that is viable for fanime though, given they have a schedule where they need to run other tournaments. They could run where the randoms are in one bracket and the premades in the other I suppose, with the end result undoubtedly going to the premade side. In that case they could cut off the top final match and make 2 tournaments.
Still any of those kind of defeat the purpose of a tournament in my opinion, putting forth something akin to a handicap in some cases.
Of course I dont work in Gaming Staff and have no idea what there total resources and end goals for tournaments are, but this is my educated guess based on what I have seen at Gaming Hall over the years.