Yeah, there was an SOS article a few years back that described a similar method, but suggested that you strip silence the real tracks. Unfortunately when you do this Logic places anchors at the transients and not necessarily at the beginning of the region, even when you set no pre attack and uncheck "search for zero crossing." This seems to me like some kind of bug, but either way, it's bad programming. Strip silence is supposedly removing audio precisely at the transient, so why would it place an anchor anywhere but at the beginning of the region? Anyway, then you would select the region and make the cut, but unfortunately Logic cuts at the beginning of the region and not at the anchor. Of course the quantize function quantizes strip silenced regions at the anchor and normal regions at the beginning of the region. The end result is rampant crazy out-of-phase-ness.
I spent months pulling my hair out over this. Finally with enough research, trial and error, I came up with this method, and it works perfectly if you're willing to spend the time.