Given how controversial SDOIT was when it came out, I’m always surprised by its legacy.
I’ll always remember the “disc 1 or disc 2” debates, and it always seemed like the vast majority were always very high on one and pretty meh on the other, but equally divided on which one was better, with everyone saying it was a half great album and no one agreeing on what the better half was.
These kinds of arguments always bother me because people are placing superficial labels on albums based on physical media limitations. Did vinyl double albums under 80 minutes get the "Is LP 1 better than LP 2?" debate back in the day, even though in the CD age the album would fit all on one disc (like The Who's Tommy)?
If CDs held 100 minutes of music, there'd be SO many less debates of "disc 1 vs disc 2" simply because the album, as a whole, would fit on one disc. This is why I like digital media because you can have a whole album of any length and not worry about people comparing two parts of what should be considered a whole album. Granted, sometimes the physical media can be used to further the concept or narrative of a double album, like having an act-break in a rock opera, or using the two discs to separate material (like with NMB's Innocence & Danger), but for something like SDOIT, the album always felt like 6 pieces that just happened to not fit on a single piece of physical media. All my digital rips of the album have been 6 tracks to fit the 6-7-8 meta-concept of their 6th, 7th, and 8th albums.
With regards as to why it's become a very popular and well-loved album, I'd say a part of it probably boils down to being one of the band's longest albums, and having the band's longest single piece in its title track. Also, I think "The Glass Prison" is a fairly well-received song, as are "Disappear" and "The Great Debate".
-Marc.