A lot of the time when JM blends in, it's because he's doubling the guitar, but more often than not, I can make out the bass guitar fine. I find modern rock/metal mixes in general tend to make the bass guitar less distinguishable and more of a "presence" in the low end, unlike older recordings where everything was more balanced without being EQ'd into such a specific register.
I can't say I really hear him on FAS, but I don't think he's doing more than doubling there either, given the orchestral style arrangement. But I can't even make out his rhythm there, whether he's playing 8ths or 16ths or whatever. For the most part, he's pretty audible on DT12, and you can make out that nice bass attack, but he still blends into the background on the heavier stuff.
I'd love to hear a DT album with a more "classic" mix, something like FII.