PHD2 is only estimating polar alignment error by measuring the rate of drift in declination. It assumes that *all* of the drift is caused by polar alignment error because there is no way to estimate the contribution from other sources. Or at least there is no easy way to factor those things out. The common contributors to drift are small movements in the payload riding on the mount - slightly loose fittings, sagging (flexure) of the OTA or various adapters, compression of the soft materials used in mounting rings or on the ends of thumb-screws, dangling cables, cable drags and pulls, the list goes on. Obviously, all of this is dependent on pointing position because that determines how gravity exerts its pull on all the different components of the payload. To visualize this, you have to come to terms with the tiny amounts of movement that the guide camera can see. Most of the common guide cameras now have pixel sizes smaller than 5 microns, some much smaller, and most people have no hands-on familiarity with measurements at that scale. If you look at the smallest interval on a typical metric ruler, that will be 1 millimeter - and that interval corresponds to 1000 microns. Very fine leads for a mechanical pencil are likely to be 700 microns thick; a human hair is typically more than 50 microns thick. These are truly tiny distances. So it's pretty hard to imagine that all the typical gear riding on a telescope mount can't contribute to unwanted movements at this scale. And if this isn't enough, atmospheric refraction will also cause apparent drift as the altitude of the target changes during the course of the night.
The important thing here is to not obsess about drift unless it's clearly causing problems with your final results. Drift is the easiest kind of problem to guide out so there's no point in worrying about a problem that in all likelihood is not limiting your results. The reason we talk about it all is that large amounts of drift may cause problems with PHD2 calibration and may create image rotation artifacts in your final images. To avoid that, we generally tell people to get a polar alignment error below 10 arc-min as a general rule of thumb. And clearly, there is little point in comparing alignment estimates from two difference measurement approaches when neither one is likely to be very relevant.
Bruce