I never understood the rotating set complaints either. Dream Theater has always done rare songs, but most of their setlist choices are just regular album tracks that they switch up each tour leg. So if you didn't see something on one tour, it most likely would appear one or two tours down the road. And with playing 3 hour shows, after a couple tours, it got to the point where they'd almost run out of songs to play, and I'd see a setlist with a bunch of songs I've seen already.
It's not like they do live jams and drastically change up songs to make each live show collectible either (which they rarely did with MP outside of the I&W tour and Hollow Years/Beyond This Life on ToT and Surrounded on Chaos In Motion and even then, the jams were almost choreographed to the point where they were the same night after night.)
It's just a bizarre argument and does not reflect the reality of just how little the rotating sets mattered in the grand scheme of DT's setlists.
While DT's setlist rotation certainly was not of the same caliber of what you're stating about DMB's and all the jam bands out there, I think you're glossing over the details.
Of course there are several songs that would make the master setlist (in other words, the complete list of songs prepped for a tour) on most tours, but there was plenty of other stuff that did not. With as much of a back catalog as they have (at this point, over 18 hours of original material), these days it would take several tours - not just "one or two tours down the road" - before songs in the catalog would appear in the master setlist again, if done the way MP did it. And that's assuming we're just talking about Evening With tours; when carrying one or more opening acts so that their sets were between 1.5 and 2 hours long, it would take even longer.
As for changing things up live, again, they didn't do it anywhere near what DMB does, but there's plenty of songs that over the years were revised varying degrees. Besides the ones you cited, what about The Killing Hand, To Live Forever (1993, 1998, 2004), Metropolis (1996-97, 2004-09), Take the Time (1994-95), Wait for Sleep (1992-93, 1995), Learning to Live (1996-97, 2005-06), The Silent Man (1995-2004), Caught in Alice's Nine Inch Tool Garden (1996-97), Lines in the Sand (2002), Solitary Shell (2009-10); the extended intros to The Mirror (1994-95), Lifting Shadows (1995, 1998, 1999), Scarred (2002, 2007), Trial of Tears and Octavarium? Yeah, in most cases, these were structured changes to the songs, but the changes always made for something new to look forward to on each tour, even if we'd already seen the song performed already on an earlier tour.
Then throw in the live only instrumentals/improvs and occasional LTE tracks, as well as the controversial covers (full albums and individual covers) and medleys, and there was even more variety added to the setlists of old. So I seriously beg to differ on your claim of the idea that the rotation of DT's setlist mattered little. Not up to DMB's standards, but certainly far more so than many other bands.