This is interesting. You're right that 3rd party chargers may not work as well as Apple's own charger, but I'm wondering if the Pencil will work at all when you're charging an iPad Pro. Do you have the charger that shipped with your iPad Pro? I'd suggest testing with that first to see if it works. If it does, then I think getting the Apple charger is a good bet.
Otherwise, I've generally noticed that charging the iPad seems to sometimes interfere with even the capacitive touch - probably because both are electrical in nature. I can't confirm it, but those are my impressions.
I'm using the Anker single-port fast charger and Apple cable with my 10.5" iPP and the pencil works fine while charging.