Count me in the camp that believes it's the perfect way to close The Twelve-Step Suite. I mean, the 2nd, 3rd and 4th songs all had parts that re re-imaginings of previous parts/sections of the suite itself, and being the finale of a near hour-long suite, I would EXPECT some, if not MANY of the main themes to come back. And I liked that they brought back more than just a couple main themes (melodies), but also some grooves and riffs, which were used with different instrumentations or parts on-top of it. It's not like they literally cut-and-pasted sections of the prior songs into TSF.
I feel like once it's played live, in the context of the whole suite, people will grow to understand it and love it. I think for some, it's just hearing it with the suite that convinces them that it's exactly what the ending should be. I know when I first heard it, I was a bit fan-boyish when I heard the TGP riffs or the TDS groove, the opening riff to TROAE or the chorus from Repentance. It was like "AHH! It's that part! Niiiiice"...
...but when I heard the whole suite together, it made even MORE sense. Hearing each of the twelve movements/Steps back-to-back made the ending SOOOO satisfying for me, and hearing the opening/ending of "I. Reflection" at the end of "XII. Responsible" made so much sense to me... and put a huge grin across my face.
-Marc.