All sorts of differences probably, but I don't know the precise orderings DC uses in its Omnibuses. Based on conjecture I read on here, I think the only diff b/w my Vol 1 and DC's is that I include Sword of Azrael and I put the Lost Pages of Bane breaking into the mansion in between two issues as a pseudo canon recap thing (vs DC I think puts it as an extra). I hear DC & I coincidentally wound up with the same ordering for the Prelude issues (well, DC didn't include Sword of Az), which if true, is great for readers.
Prelude order should be this:
Sword of Azrael
Vengeance of Bane
Batman #484-487
Detective Comics #654-656
Batman #488
Detective Comics #657-658
Batman #489-490
Batman #491 (is in all Knightfall tpbs, so don't even count it as prelude anymore)
I probably integrate The Search into The Crusade in Vol 2 in a different way than DC does. I think I found the best way. If DC kept the two separate in the Omnibus, I really think that's silly, but I doubt they did that. But I'm curious to know what order they did use to integrate the two.
My Vol 3 roughly looks like this:
old Knightsend TPB content
Batman #0
Shadow #0
Tec #0
Robin #0 (real part 1 of Prodigal)
the rest is Prodigal
Troika
Azrael #1, Azrael #2 (Az #1 and pages 1-8 of Az #2)
Nightwing Alfred's Return
Veng of Bane 2