Possible D5100 focus issues

Took a brief look through your photographs and, indeed, the top of both images seems to be quite similar, but the bottom of the PDAF one gets increasingly worse. That's... weird. I mean, I can find a few reasons for it to happen, but if you didn't touch the camera between shots, all of them would apply equally to both PDAF and CDAF.

Was your camera completely, perfectly, perpendicular to the chart? Focus is a straight plane, and if the camera wasn't perfectly perpendicular, the focus plane would bisect the chart, rendering part of it in-focus and part out-of-focus. Again, this would apply to both AF methods.

If your lens has a misaligned element, it could change the geometry of the focus plane and achieve that effect, as well. That would mean ALL your photographs would exhibit this to some degree.

I don't know. That's really weird.

CDAF hunts back and forth until it finds optimal focus, so it will, theoretically, always have perfect focus. Obviously, if there's any problem extraneous to the focus system itself, the focus won't be as good.