I was able to accomplish this by simply switching the time signature at the bottom between takes by doing a little math first.
For instance, I created a piece of music in 13/8 time, then wanted to pair a another track in 4/8 (yes it was insane).
The lowest common multiple of 13 and 4 is 52, so I set up a 52 measure block of 13/8, then switched the time signature to 4/8 and played that part, using the metronome for a click each part.
So with this in mind, and perhaps even more useful for "live" recording, another option is to use the metronome and render the click tracks you need beforehand - spend some time playing with the metronome and creating the right click track for what you need. Render it to a track, then switch the time signature and render another one. Then you can switch with the mute button, or even set up an automation to control the switching between them automatically as needed. It literally took seconds to set up a few click tracks of different time signatures to create any imaginable polyrhythm.
