I don't agree with the notion of Beautiful Agony needing to be two separate songs. It's full of references to the main song, is connected lyrically to it, transitions smoothly from & back into it, & largely works because of how well it contrasts. Isolating it would make it into a Wither clone & would take away what I find special about it.
I could understand the argument of thinking the solo tradeoff should've gone straight into the final chorus (cutting 10:28-13:20), but I disagree with that too. I think it works fine as it is, because the heavy part adds more variety & the riffs afterward make the transition to the final chorus smoother.
I think ANTR handles its length a lot better than disc 1 of SDOIT, most of TOT, & the Octavarium title track, personally.