Is there any limitation to using PHD2's Polar Drift Alignment tool with a single axis tracker like my SkyGuider Pro? Also, should dither settings be set to RA only?
By single axis tracker you mean a mount that will only track the Ra axis, not the Dec axis I suppose? Can this tracker guide in Ra?
If so you should be able to configure PHD2 to guide in Ra only and that should be enough to enable the PHD2 drift polar alignment. If you can't guide at all then PHD2 may be unable to do anything.
Just set Dec mode from Auto to Off. You can do that at the bottom of the window or in the brain under the algorithm settings for Dec guiding. If you don't disable Dec, it will never complete calibration.
I don't believe you have to make any special settings for dither when in RA only. But you may want to consider manually moving the star tracker in Dec occasionally to avoid a drifting noise pattern.
What focal length do you intend to image with? If shorter than, say, 250 mm then I’d not worry about very accurate polar alignment. Just use the polar finder of the mount and you should be fine. The other day we used a SkyGuider Pro and a 135 mm lens. Over the course of 4 hours there was significant drift in Dec but the stars were pinpoints.
You can use PHD2 Polar Drift alignment with an RA drive only mount. In fact, none of the polar alignment tools move the mount in declination. And even RA movement can be performed manually.
Without Dec corrections drift in declination could be an issue. PDA is not highly accurate for PA (within about 10 arcmin) so you might want to follow it up with a classic drift alignment or SPA.