This is a non issue to me because now I know to turn off tracking correction should I use the automated 3PPA in Nina. That should be done anyway as Ray pointed out.
As far as I can tell other move commands in NINA work fine. The only other instance where NINA moves the mount is during framing of the target. I believe that uses the slew command, not move axis and I didn't see anything unusual happening during the framing process.
In the custom rate setup in APCC I tried to change it to "relative to zero" and "relative to sidereal" but that didn't seem to make any difference.
I also tried the move axis command without APCC, just using the AP V2 driver, and that always worked fine with both the CP4 and the CP3 V2chip (with the CP3 I had to choose a rate of 4 or less and that is expected).
So in essence for my specific use case I am happy with the current software and drivers as they are.