Except have you been able to write freehand with PDF Expert? I have it and while I can highlight a PDF with the Pencil, it refuses to let me write freehand with the Pencil (no "ink" is drawn), though I can with a finger or passive stylus.
No I don't have an iPad pro so I don't know. I wouldn't want to do much handwriting in PDF experts as its not a very smooth experience, but for small notes it's okay.
In my experience, PDF expert is great for PDFs, and goodnotes is great for handwriting.