Jesse!! What a great question.
Yeah, I love to “cover my bases” for mixing options later by capturing a great close mic’ed sound (mono or stereo) and supplementing with room mics, which can be balanced to taste later during mixing.
When placing the room mics (and all mics for that matter) I try to ensure that their signal is recorded in phase with the close mics — and also with each other, which you could check by soloing the room mics and flipping polarity on one of them to see if the sound gets better or worse. One advantage of XY stereo mic’ing and other ‘coincident pair’ mic setups is phase btwn the two stereo mics becomes a non-issue. With the capsules right on top of one another with a 90º angle, it’s near impossible for the phase btwn the two mics to be anything other than glorious.
Once your room mics are sounding good on their own, any phase discrepancies btwn the room mics and the close mic(s) can be adjusted by physically moving the room mics closer or farther from the close mic until all the mics blend together in a positive/additive way.
NOTE: when checking phase like this you always want to make sure all signals are playing back at roughly the same loudness. Even if you know you’ll likely bury the room mics at a low volume beneath the direct mic, you gotta turn up the rooms so they’re as loud as the direct mic(s) to hear the cumulative effect of flipping those polarity buttons in or out.
As for time-alignment of the room mics during mixing, that’s not something I do regularly at all. Once in a while I’ll scoot room mics earlier on the timeline (or later!) to get a desired effect, or if I like the room sound but sense that the mics were really placed farther away than I would have liked. (And, importantly, this trick would only work if there’s no bleed from other instruments in the room mics you’re moving, otherwise you’d screw up the room sound and phase relationship related to those other instruments).
Honestly, the only times I can recall doing radical time alignment on room mics like that is when I’m mixing live performances and the front of house mics or other ambience mics in the audience are creating too much of an echo effect against the direct stage mics because those mics were literally hundreds of feet away from the stage.
For day to day studio room mics and whatnot tho, I will definitely throw a time adjuster plugin or Little Labs IBP or SoundRadix Auto-align on there and do some sweeping micro timing adjustments if I feel like I can get the phase relationship tighter. And importantly, this method a) is only delaying the signal by samples or milliseconds, not seconds; b) does not move things earlier, only later in time, which is why I tend to use these plugins on the close mic/DI as opposed to the room; and c) will keep your audio clips at their original position on the timeline, which I’m always in favor of when it comes to time-alignment. Otherwise I’m libel to accidentally move some clips more than others and/or forget the specific offset I used when moving them, etc … all sorts of potential gremlin nightmares arise haha.
Ok that answer got a little long! Hope this all makes sense and is helpful, you rockstar!