I appreciate the problem, here. It is my practice to eliminate all body detail features such as door handles, wipers, door locks, etc during body prep (scripts and detailed side trim excepted) to facilitate cut & polish of the paint, and re-create them later. There are a couple of options for replacement 'printed' rivets, both self-adhesive and printed on decal film. I would be tempted to (or at least, tempted to consider) remove the rivets and develop a solution to restore them onto finished paint. There is no doubt this would be a huge nuisance, and one would have to consider carefully how to proceed before beginning (such as experimenting with the various rivet sources available, mapping or photographing the existing rivets before removing them, develop a method of installing them accurately).
In the end, that all seems a bit much. One might only do this on a high-end project, and is probably much more work than 99% of builders are willing to undergo.