Okay. The key steps are these:
6. Select only the drum overhead track.
7. On the AudioSnap palette, set Threshold to 100% to ensure that there are no transients detected. This step is necessary because the overhead track contains audio from both the kick and the snare, and you want to make sure the kick, snare and overhead tracks are always synchronized when stretching beats.
This is not clearly stated. The goal of disabling markers on the overhead track is to prevent it contributing duplicate markers when Merge and Lock is executed. If you did that, and still have duplicate markers after Merge and Lock, then I would guess there was enough bleed of the snare in the kick Mic or vice versa that you got some duplicate markers that way. You can use a combination of Threshold controls (each track can have a differnt setting) and manually enabling/disabling/promoting markers on the kick and snare tracks to make sure there's no duplication before executing Merge and Lock. It's also possible to have markers for 'false-positive' transient detections within a single track that need to be disabled.