e.g. your speakers are out of phase when you have one speaker with positive and negative outputs on the amp going to the positive and negative inputs of the speaker, but the other speaker has them reversed. That's as much as I know...

Thus, I assume that pickups out of phase are the same, where you have two pickups selected and one of them has the polarity reversed in relation to the other.

If that's what you mean by "phase shifting".