Same issue with chrome browser on Surface Pro with pen, works mainly ok with the touchpad on same pdfs, on same browser. All in all, Surface pen and Paperpile not working together almost at all, drawing/highlighting by drawing (instead of long-press+wait) requires side-button press which is practically not possible. The little I revert to pen-based commenting happens now with Xodo pdf-reader, where it works decently.
Well, I decided to invest on iPad Air and Pen now, as the need is significant enough. I hope it works better.