I'll admit I wasn't exactly thinking too hard about copyright issues regarding that music. That being said, this is part of the discussion phase, it's not like I've already generated PCMs of the albums in question. (I'd probably need to end up purchasing them to begin with, anyway, considering how few people actually rip music in a lossless encode nowadays.)
If you're worried about copyright, we could possibly just set up a document or program to convert the CD album tracks (from an actual CD) to the game-appropriate PCMs. Personally, I don't feel like my proposal is comparable to, say, the idea of using the original licensed songs in Rock n' Roll Racing, but I can understand if you're against it on principle.
(EDIT: I would also like to point out that technically the Mega Man X 3 PCM set using music from the PSOne version would fit the description of "piracy" just as much as using an album source.)