[Stig Eliassen]

1a) If you bypass the reported delay on a track this delay is left out of the equation when PT aligns the audio output of all tracks. So this track would now be delay compensated by the largest reported delay in the session, but its own delay will not affect the session.

1b) If you bypass the delay compensation on this track it will not be compensated by any delays at all in the session.

1c) It really doesn't make any sense (to me at least) to bypass both the reported track delay and the track delay compensation. If you have a plugin that reports a delay that's incorrect you simply bypass the report and type in a user delay instead.
If you could bypass both it would lead to a scenario where this track didn't report its own delay, and it wouldn't be aligned with the other tracks in the session.

2) They turn blue? Haven't seen it - must read up on that one. I have heard that stems have been wildly out of sync during printing, but synced as normal after printing when playing back. Could be what you're talking about.