Let's get something basic out of the way... stlyli don't scratch the screen but grit that gets trapped under the tip of the stylus is what can scratch. (keeping the screen clean is important, but you have to make sure the stylus tip is clean as well)
I'm using the Apple Pencil on both a 1st gen 12.9 iPad Pro and 2018 iPad. Neither NEEDS a screen protector. I used the 12.9 Pro without a protector for well over a year, nearly daily with the Pencil, and no scratches.
But I have applied matte screen protectors on both... to cut down on reflections and visibility of fingerprint smudges but also to offer an ever-so-slight resistance for the Pencil.
Without a screen protector, I find the Pencil to be too slippery to feel natural. The matte screen protector helps a bit with that. A common criticism of matte protectors is that they interfere with the sharpness of the display, but by using a good quality protector that effect is minimized.