Doesn't it kind of contravene the spirit of a national training centre for it to be built in conjunction with a team? The point of a training centre is not just to have some usable facilities for anyone who wants to book it to use, it's to provide a nationally-run and nationally-focused academy producing top talents for the national side. It's supposed to be neutral and non-club-affiliated in order to stand as the central hub of academy training. If you then make that facility a partnership with a specific club then don't you open up the USSSF to all kinds of accusations of bias?
Imagine this scenario: Player A lives in City B, which has an MLS team, but City B FC have an academy which still operates on the basis of pay-to-play, and Player A cannot afford the fees. Under MLS rules, teams have an exclusivity area which prevents other MLS teams from poaching their talent from under their noses. Player A - as an outstanding talent - is, however, eligible to join the elite USSSF National Academy in City C, which has been built in partnership with FC City C. Player A graduates and USSSF, in accordance with the terms of their agreement with FC City C, encourages him to sign for FCCC, where he qualifies as Homegrown. City B FC now find that FCCC has managed to poach a player from their city in contravention of the rules by virtue of FCCC's exploitative partnership with the national federation, and takes them to court.
Surely a national team centre would have to be non-affiliated for just this kind of reason?