Phase incoherencies and comb filtering from delayed signals are not necessarily one and the same thing. If say the fundamental frequency is 180 degrees out of phase between two mics, you can shift the signal of one of the mics half a wavelength and that solves that. But the harmonics have different wavelengths, and now THEIR phase relationships have changed as well. I don't know, however, if the phase problems with micing guitar cabs are generally just from differences in distance (disregarding the room reflections here). I could imagine that if one mic is angled it would introduce some other phase issues.
There is a trick regarding getting mics phase aligned (maybe?). Pull out the cable from the amp, crank the master volume till you hear the hiss clearly, put on good isolating headphones, flip the polarity on one of the channels and move the mics until the signal is as low as possible (probably won't be gone completely). Then un-flip the channel again and bingo.