That's what I did on these. Didn't seem to matter. The paint issue really isn't caused by the rotational friction, but by the deformation of the paint film due to the fastner pressure. On these upper hinge screws, I held the screw stationary and tightened the nut on the back. On the lower hinges I had to tighten the screw, and it actually wasn't as bad. The counter sink bit is a good thought, but then I'm looking at black hinges.What about just dabbing the holes with touch up paint during installation so it serves as lube for the fastener and seals any rippling/chipping/peeling? I'm not a paint expert, so if there's something inherently dumb about that, I plead ignorance.
I would get a counter-sink bit to match the angle of the new hardware, personally. That would both touch up the chatter and also give you better fitment with the new screws.