What I was using (some cheap board) didn't have good resolution for measuring the incoming PWM (it was +/- 3-5% so the voltage measured in the output was bouncing up and down and in turn the square wave output of the Arduino was looking like a slinky on the oscilloscope). I didn't take any screenshots so nothing to show but I just ordered a Nano 33 loT which has a DAC (digital to analog conversion) output, so I can do some proper testing and report back with some data.
I still think it makes more sense to use one board to do everything, but I will do some testing with the Nano's DAC as well as trying out all of the other fine suggestions I have gotten regarding timer use.