PHASE ..ers set to stun. Drum replacement especially or drum mics top and bottom ...

papacucku
I thought I saw something like that somewhere?  like even though the transients and wavs are perfectly alligned they can be out of phase I think.

If the transients are "perfectly aligned", then they are, by definition, in-phase.
 
You cannot ever truly get two microphones completely in phase for all frequencies, though, as each frequency has its own phase relationship due to different wavelengths. Because it's physically impossible there is also no plugin that can do it, either.
 
You can adjust the phase relationships between the snare and overhead microphones by ear the same way you tweak dual mikes on a guitar cabinet. You're always going to get some cancellations, but some phase cancellations are less obnoxious than others so some experimentation is required. There is no set formula, and it'll always be a compromise (don't forget the tom/kick/hat mikes).
 
And you're right about the pro's not ignoring this, but they usually resolve it with mike placement rather than by editing the recorded tracks later. That's one reason you see permanently miked-up kits in studios - they get it all just so and then don't mess with it again.
 
You can also see why some hard-core old-schoolers insist on using a minimum number of microphones on drums, some preferring a single mike up high and another on the kick and that's it. It does simplify things greatly.