Right, I'd be remiss if I didn't mention the irritating fade-out at the end of "Persecution." It starts way too soon and ends the track in an unsatisfactory way. I'm sure other edits were made to the track, but I found the absent effects and the fade-out most conspicuous.
For comparison, here's what the digital track listing looks like. Note that even though some tracks are shortened, "Omni_00" is actually longer: