I find that hard to believe. I've done plenty of testing and the custom eq does NOT affect mp3's. Leave a flat digital eq activated, start playing an mp3, and while it's playing, go into custom eq, crank all the levels and activate it. You won't hear anything change.
The reason this is a half-ass implementation is not because of the digital eq itself, but the way it's thrown in there for the mp3s. Now, if I want to use a custom eq for ATRAC, I can. However, it means the mp3s will always play flat (until I change the settings again). So, we're basically forced to use the digital eq since it will affect both ATRAC and mp3s. This was just plain dumb, but that's typical Sony for you.