Quantize moves things to the beat and by moving all the audio together, you don't really need to worry about phase issues. At least not ones introduced by Audiosnap. ;)
I've been following this series and although I think it is a perfectly workable method, it still seems more complex than the method I used in Reaper for our last album. I did everything in Sonar except the drum editing, for this reason.
Reaper makes it easy to split a clip and create a crossfade at that point at the same time. This then makes it trivial to adjust the hit. You can drag it forward in time, the clips become separate, a fade out then a fade in. Or you can drag the hit backwards in time and again the crossfade covers the overlap. Sometimes you'll drag the audio within the clip (rather than dragging the whole clip) to avoid making the crossfade duration too large. But the essence of it is, for each hit there is one click to split, one drag to align, done.
In Sonar, I don't know of a way to split a clip and create an automatic crossfade. That changes the workflow significantly and is part of why, at the end of part 3 of this series, you still have hits cut off at the ends (
http://blog.cakewalk.com/wp-content/uploads/2014/11/m22-23-aligned.jpg) which will have to be fixed one way or another in part 4. It's not a big deal when you are just working with kick/snare/hats but when you have a crash that you want to sustain through 5 or 6 beats, you're just going to have to go back through the overhead tracks and edit them all back to full length, cross-fading with each of the previously-split clips.