Column render sounds like a great idea. When I was originally suggesting clip render, I too thought about the timings and things getting complicated. Which is why I asked for the simple clip render.
Maybe the only approach to times that don't loop evenly could be a time stretch. Meaning, change your playback time of the clip to an even multiplication or division of the longest clip. Then use a video router to capture all the layers below? Then Clip render on the Video Router? Looks like Clip Render is greyed out for that.