The answer is absolutely YES. PDF Reader Pro works well with Apple Pencil in different aspects. You can use either of the two generations of Apple Pencil with PDF Reader Pro on iPad. It has full pressure sensitivity for dynamic line thickness, palm rejection for full sketching, and works as a simple stylus if you don't want to touch your screen.
Also, the second-generation Apple Pencil has one added function, which is accessed by double-tapping the flat side of the Apple Pencil near the nib. You can choose one of the double-tap functions from Switch Between Current Tool and Eraser, Switch Between Current Tool and Last Used and Show Color Palette in Apple Pencil Settings, then use it freely when you annotate PDF in PDF Reader Pro. Turn on Scribble and you can handwrite in any text area to convert it into type.