I say this respectfully, but - and it's a similar criticism that comes up about the Iron Maiden album - I don't follow the "cutting". One can, of course, make a playlist, and there are albums I do that for, certainly, but for me, both of these releases are, because of their scope, more than just a "collection of songs", and so for me, they are what they are. I think "Emergence" is critical in terms of pacing, and while I can (and do!) sometimes skip to songs (I just need to hear "Bird On A Wire"!) if I'm listening to the album, it's a sequence.
I like how both albums start with shorter, punchier songs, set the tone then progressively (ha!) move to more complicated, more involved pieces. They work in that context. I can't imagine just a NMB album with, say, CD1, or just an album with Not Afraid Part 2 and Beyond The Years. The album is balanced out by the songs on both CDs. Likewise, it's not the same album if the new Maiden record is just "Darkest Hour", "Death Of The Celts", "The Parchment" and "Hell On Earth".
By the way, I don't suppose the connection is purposeful, but I love the overlap between Maiden and the Neal Morse universe with the "You sowed the wind, and now you reaped the whirlwind!" reference in "Darkest Hour".