Yeah, you need the markers to be at the same place across all tracks and move exactly the same, which is the reason it's all added to the pool and the pool is quantized, or yeah - you get terrible phase issues everywhere.
You really don't need to create separate detection tracks if your drum part is fairly simple - most rock stuff is, most prog metal is NOT - you should be able to get clear hits on kick and snare without them getting overlapped or confused. The other reason you may want separate tracks is to do transient to MIDI conversion so you can overlay drum synth samples. If you don't need to do that, save yourself a step and bounce both your gated tracks down to one.