"Fixing" screw holes for rear soft top bar?

Have been doing some teeny "body work" (cleaning and painting screws & bolts, priming and painting little rust spots). I decided I don't want it sitting all winter so I'm going to put the soft top on. I bought a new bar for the base (comes with new screws) but the existing screw holes are both protruding and rusted (see front, side and view-from-above pics). I am wondering if they are raised for a reason and if I should leave them alone (just remove rust, then prime and paint) or actually sand the metal down so they're flush with the area. Anyone? (And if it's rude to post giant pics, let me know.)

 

Welcome. I think why the hole are not smooth it is where the screws were tightened and the screws pulled the metal that’s why they are raised not a big deal my opinion let’s see what the other day.

 

When the metal is pulled out from tightened bolts sometimes light strikes with a flat faced hammer can push some of the metal back. Some of the tools in the pic may be useful if you have access to the backside of the deformity. Flatten>sand>prime>paint

 

Wouldn't it just be easier to just eliminate the rough edges from the outside? The holes don't seem to be deformed; the screws do still fit. Or am I missing something?

 

That’s what I would do just sand and primer and paint