If the issue is between Neal and Roine, I doubt it is over religion, but over way the Neal did his shortened version of The Absolute Universe, which saw him remove quite a bit of Roine's best stuff, not to mention adding a song that Roine didn't even play on (Can You Feel It). I am sure Neal's intentions were noble, and a couple changes were for the better, but if I were Roine, I would have been pretty ticked. Neal deciding to remove The World We Used to Know, the centerpiece of the album (and the best song, IMO), just boggles the mind.
I've always seen this situation the same way, with Mike trying to play peacemaker between the two by suggesting they release both versions - Roine's original, longer idea of the album, and Neal's truncated/re-done version, and while he was at it, make his own version that combined his favorite bits from both while making it longer than either.
It definitely struck me as ironic when Neal was the one who wanted to make the album shorter and Roine wanted it to keep it a double, but I think Neal was maybe worried that he would be associated with putting out so many double albums in such a short time (after TSOAD and TGA came out). There's always going to be more than what we'll ever know about that situation and what their personal feelings were at the time, but I think at this point they've probably mellowed out a bit, but are not likely to reunite any time soon, and it definitely feels like TAU will be their last albums.
As far as how their catalog ranks, it's easily one of my favorites, and while their last two albums feel like a bit of a rehash of their earlier works, it's like being served a really good burger and fries instead of a steak and mashed potatoes. Sure, there's almost the same, and earlier steak and potatoes are probably better than the latter burger and fries, but both are good meals regardless. I think throwing in the towel after album and tour number five was a good call over-all, as they've definitely said all they need to say with their music.
Now, if they do a one-off show in the future, I would not put it past them. Neal would most likely initiate that conversation, but it would probably be part of a festival or a cruise, where Mike, Roine, and Pete also happen to be there in addition to Neal, though given how old they're all getting, and how sporadically everyone but Mike seems to tour, I wouldn't hold my breath.
-Marc.