Keep in mind that bands retrospectively admit issues in their material all the time. When Sanctuary just released their first album in two decades, almost every interview with them saw them mention how awful the production on their two earlier albums were and how much better this one is (as an aside, if DT12 sounded like that album, it would have been much better off). Even with DT, there's the FII issues, there's the Prater issues, there's Petrucci calling WDADU amateurish, etc. Hell, there's even the infamous moment where JM calls out the move-into-the-studio-and-write stuff on the WDADRU commentary. Obviously they're not going to take shots at the last album, because it's their newest product and they're still trying to sell it. I wouldn't be at all surprised if in a few years, some interviewer could wring an admission from JP that DT isn't exactly their best-sounding record. Heck, MM has already hinted at this, though not in a particularly negative spin.
Again, if it turned out that JP really did consciously decide every thing and couldn't possibly be more satisfied (as well as the rest of the band), then sure, that's his artistic integrity and you have to respect it, etc. But without that affirmation, it's fair game. If you go to a DT show with a friend, and James sings a bunch of notes flat, and your friend turns to you and goes "Man, James' performance really hurt my enjoyment of the show," you don't go "Hey, that's the way he means to sing it!" Of course he wants to sing the notes on pitch, but sometimes he doesn't fully get where he wants to go. It is entirely possible that the production of the newest album(s) suffered a similar issue (granted, not a great analogy, because you have time to revise production as opposed to one chance to get a note at a show, but it's the same idea).
I have no doubt that some of it is Petrucci's preference, mind you. I can't say I know much about the Steven Wilson stuff everybody brings up as a polar opposite to the DT production, but just from what I can infer about this Fear of a Blank Planet thing, I'm quite sure JP is going for a louder, less dynamic album than that with DT12. That much can't be questioned. But the subtle nuances and errors of the production beyond that? I'd be willing to bet that if you took another metal band's album to JP, and you played him a loud but well-produced version of it and a Death Magnetic-type produced version of it, he'd prefer the first one. Much like James hitting many notes at a show but missing a few, JP could well have gotten into the general range of production he wanted but may not have found a way to better it further, even if he would have liked to.
So in sum, asking JP to change his production preferences just for your sake would, yes, violate artistic integrity to some degree. But since we all assume that his production preferences involve some sort of good outcome (especially with him going on about the chocolate cake stuff the last album cycle), it's entirely reasonable to think that he wouldn't find the product devalued by a simple reduction of the objective mistakes, etc. Unless there's clarification as to what made these issues happen, it's totally fair to question them.