lets discuss,
will it affect operation?

But why?

I cleared one,worked for years and still worked before I pulled it for an upgrade.

As you know 90% of sucessful painting is in the prep (cleanliness/right grit of surface sanding). wouldn't affect operation. You'd wanna take it apart to do a primo job

I prepped one really well for paint once and got a great paint job on it. Prep included spray solvent to get it clean. Later I found that spray solvent and the insulation on the wires inside don't get along. The alternator failed on a road trip. I got home but its a very long (and fun) story. My advice is to either leave it alone or buy a painted or plated alternator from a rebuilder or new. Don't try to DIY.