John,
If you have a decent sub-woofer, the low organ notes ARE sufficient at the end of Part II. But you're right: the organ is fuller sounding in Part 1 than in is in Part II. It's hard to guess if this was a deliberate choice on Boulez's part, or if things just happened to turn out that way. Remember, they basically rented an electronic organ for the recording sessions. What bothers me isn't a lack of bass at the end of Part II, but rather that the upper notes of the organ are not very audible. I believe that that might have a been a deliberate choice in order to make the offstage brass sound clearer. I frankly feel that it's very nicely balanced, but would still like to hear much more of the tam-tam at the end.
It seems clear to me that Boulez wanted to make the concluding "Gloria" to Part 1 as grand and vulgar - in the good sense of the term, "vulgar" - as humanly possible. That being the case, I think he made a deliberate attempt to make the end of Part II sound different. Something's lost, but something's gained as well. For example, I really like how he allows his trombones to just crunch those octave harmonies near end of Part II, just before the final series of cymbal/tam-tam smashes. I also like his slower than normal tempo.
In the final analysis, I agree with you: it is slightly frustrating. It would be nice if Euroarts could issue a DVD of the live performance from the Philharmonie, just as they did with the "Resurrection" (vastly superior to his Vienna one, in my opinion). But you have to give credit where credit is due: Boulez has taken a giant stride in making the mighty 8th more musical than it usually is, without also making it really boring (Abbado!). I really love the grand spectacle that he makes of Part I's ending; and, I like how he lets his trombones go to town near the end of Part II. More gong would have helped a lot.