As Fly4Business says, the iPad Pro (with Apple Pencil) works really well for making notes in freehand on any PDF document (notwithstanding you have a relevant app, say Fluix etc.).
Of course, whilst we can do this, it's also a matter of (for those of us living in the world of EASA, AOC Ops.) satisfying the criteria laid down in AMC 20-25, TGL-36 etc, and gaining approval from the CAA....and this I know only too well, can be where the various "problems" can occur....been there, done that, doing it currently...personally I'd like to see us have the ability to complete the OFP's etc., using the Apple Pencil, and then return electronically (email, submitted form) with all other paperwork (photo's of tech log pages inserted in relevant areas of forms we've created etc.).
As for Jepp's FD-Pro, as great as it is, getting AMMD approval (ETSO-c165a) is a bit of a nightmare to use the aircraft symbol as depicted, using the in-built GPS receiver of the iPad....because the accuracy just isn't good enough when overlaid on Taxi Plates (10-9, 9A etc.), and you can find the aircraft symbol just isn't where it is supposed to be...maybe an external aerial would fix that, but hell of a cost implication for STC's etc. - maybe a window sucker internally might work, but again you have to prove a safety case..
As it was once said "I have a dream" haha....but it's coming along nicely...
F/o