Someone can correct me if I'm wrong on this, as I am not an expert by any means.
The basic jist is that one of the biggest acting unions
has a rule where you
have to work under a union contract. This rule is the source of controversy, because on one hand it's aimed to ensure that the actors represented under a union are fairly paid and represented, but on the other hand it can limit work because some places are not union members and do not pay their fees for whatever reason. Atlus, for example, apparently does non-union work.
Buuut under US law, you can
claim financial core status, and work on non-union jobs, but only after you've paid your dues to the union and such.
As Troy Baker has done bigger name works, he probably hasn't been able to claim final core status, and thus hasn't been able to reprise roles in Atlus games.
In the 90s, working under a pseudonym was a common way to get around this issue. That's why you'll see some actors credited under different names and stuff on a lot of anime.