This is why recording drums can be really hard. Phase can definately be an issue when micing drums. Generally I take the time to make sure that the overheads, kick and snare are in best phase as I can get them. Then throw on your tome and hat mic, plus whatever. As stated before, the fewer the mics the fewer instances where phase can kill the tone. However it is difficult to get some drum sounds with only three or four mics. This dirrectly relates to how good a room you have to record. IMHO the deader the better. The cleaner and tighter the drum recording, the more freedom you have in the mix. When the drums sound like they were clearly recorded in a garage, well they are never going to sound like they were not recorded in a garage. This often leads to over micing the set, on top of poor acoustics and so phase, phase, phase. If possible I will mic the crap out of the kit, but only use what I need in the mix. This may include room mics and various mics around the kit. It is ultimatley decided by the type of music and what fits the song.
So back to phase. If this recording is important, hire a good engineer. Use as best a facility as you can afford. You as the musician should not be concerned with phase. In fact if you are bugging the engineer about phase you are wasting his time and your money. If he is good, you won't have a problem.
I have time aligned tracks in Pro Tools, if you are carefull it can actually be quite useful. For one reason or another some times stuff gets tracked out of phase. If the guitar cab has multiple mics, lineing them up, or even messing with the alignment can bring out the tone, or make is sound like ass, just gotta use your ears. I have also messed with the alignment of the room mic, results varying of course.