I often find that conductor will commit updates to the files in the "conductor" directory in the same CL as the code that it generates as part of the track it's executing. My ideal work flow would be to commit only the output of the track in one change, and then in an immediate follow on CL commit modifications to the conductor state files. This simplifies the process of code review and separates the artifacts that are generated from the artifacts used to track progress.
I have attempted to do this by modifying some of the md files that instruct conductor how to commit and track work. I have had some limited success but have yet to arrive at a reliable way to separate the code generated by a track from the track management.