Bus Latency ?

PDC depends on the plugin itself to report back what its internal latency is, so that Cakewalk can slow everything else down to match it. 99.9% of the time, the scheme works perfectly. It's one of the details that CW worked out long ago, before most other DAWs did.
 
Once in a while, though, a plugin isn't accurate in its reported latency and phase cancellations can ensue. Sometimes external hardware can also be an issue because there is no mechanism for it to report its latency back to the DAW.
 
It's easy enough to test a plugin by sending a sharp transient to it and zooming in on the waveform to make sure the main and parallel paths line up.
 
The only time you're going to routinely run into latency problems is with plugins that feature minimum-phase filters, meaning any equalizer or any effect that incorporates an equalizer. For that reason, you want to be careful applying EQ to parallel paths and avoid steep EQ boosts. Or use linear phase equalizers. These issues do not normally apply to compressors, even if the compressor incorporates a sidechain filter.
 
As for when you'd want to intentionally defeat PDC, I can think of only one scenario: when you have to track something new on a nearly-finished project, such as a last-minute BGV. In that case, it's acceptable to temporarily kill PDC for the sake of synchronization while tracking.

That's a common challenge when layering sounds. Phase relationships between the layers can both increase and decrease tonal complexity. When it's a bunch of human voices or violins, it usually comes out sounding pretty good. When it's layered kick or bass samples, it's a toss-up. The difference often comes down to the frequency ranges and the inherent complexity of each layer. Higher frequencies and more complex sounds (like voices) tend to blend better.
 
Fact is, you cannot get two drum samples to ever be perfectly in phase with one another. Not unless they're literally identical, which would indeed defeat the purpose of layering. That's because you can only ever match phase for one specific frequency and its harmonics. The more inharmonic content there is (e.g. drums), the more phase differences will exist.
 
That said, it's still worth fiddling with phase to see what effect it has. It's why you use two microphones on a guitar speaker and move them around until you find the tone you like. It's why you nudge drum or bass samples and listen for when it starts sounding fatter. Superior Drummer does let you offset the X-Drum sample for that reason. In the kit definition screen, enable the envelope section. There is a knob labeled "offset". The knob's overly touchy though, so you may want to type in offset values since you'll likely settle on a value of just a few milliseconds.