I was scanning the FB Production & Post-Production Sound for Film/Video group and found a discussion on Aligning phase in the polyphoninc dialog tracks. A lot of it was a rehash of a jwsound posting, but part of this reply popped out at me.
I use Premiere/Audition, and when you Merge Clips (audio waveform matching just like PluralEyes), the waveforms are automatically time aligned to the best of the computer's ability. For mics that don't move a lot, that means you can blend them, no problem. I often throw down a plant mic for the purpose of giving me a 'reverb/room' track that I can blend into the lavs, which I find can often help match to the boom. If you instead use timecode or a camera scratch mix to sync your sound, you'll get phase issues either from speed-of-sound * distance or digital latency, all of which can be compensated for either with input delay on the day, or dealt with in post.
Would all of the polyphonic tracks be aligned to be in phase ? Seems unlikely to me.
Al