I can confirm. I was thinking of buying an iPad Pro with an Apple Pencil for this exact purpose - PDF annotation on Moodle. I borrowed a friend's to try it out and uploaded a test PDF.
There are two issues I noticed:
- Stamps - using the Apple Pencil, stamps appear below and to the right of where the Pencil hits, i.e. the top left of the stamp is where you placed the Pencil. You can get used to this, but wouldn't it be better for the center of the stamp to be where the stylus is placed?
- Annotating (lines, circles, etc.) - if the PDF can scroll, it will scroll. Thus, the only way to draw a circle is to have the pdf scrolled all the the way to the top, place your stylus, and draw a circle UP (the PDF cannot scroll up). Or scroll all the way to the bottom and draw a circle DOWN (the PDF cannot scroll down). Same with lines.
I can confirm that this is a Moodle problem. I've also tested it on my Fujitsu T-902 tablet laptop with a stylus: stamps are still misaligned, and while the lines/cricles/annotating works marginally better, it is by no means controllable or easy to use. It seems the only way to do it right now is with a mouse through your browser.