Unless I'm mistaken, the USSF training center is used specifically for national team activities - it's not used as an individual academy that anybody can join, rather a location for each pool of age-group NT players to gather at when camps are conducted.
In the past, it was at a Chula Vista - using the USOC facilities - and then it was moved to Carson, Ca in a partnership with the (former Home Depot) StubHub Center (LA Galaxy) in 2003. This helped to cut down on overhead because facilities were shared and the USSF didn't need them every day of the year. Additionally, these locations were used because most of the US coaches were based in CA (Bora, Sampson, Klinnsman) and it was convenient to fly to Central America. Bucking the trend, when Arena first managed, he was with DCUnited and the MNT had a lot of camps on the east coast rather than go to a Chula Vista.
I guess one could argue that it provided an unfair advantage to the LA Galaxy, but really USSF was just another tenant paying rent and using the facilities. Any team could conceivably do that for the extra revenue. Personally, I think that if an MLS club wants to enter into a partnership with USSF, and in doing so have essentially a cathedral for training albeit one that is not 100% their own, then I have no problem with it. I would expect their stadium to also be used as a "national" stadium for many games. If not for the Field Turf at Mercedes-Benz in ATL, I could see Atlanta being the landing spot as that would be a ridiculously amazing venue for high profile matches, convenient to the West coast & Europe, a monster airport with routes everywhere, and perfect weather for training.
Sure, but the article quoted says that USSF are considering building a facility "like Clairefontaine", and the FFF definitely run Clairefontaine as an academy in and of itself. In fairness, the article also cites Coverciano, which I thought was another national academy but apparently is just the Italian training base, so perhaps I am wrong after all, but the mentioning of Clairefontaine gave me the impression that the USSF had bigger ideas.