My #1, if not-too-Autopian

answer is to just live with `em. I`ve let them go for many years (decades in the case of the Jag, before my painter got fed up and fixed `em gratis) with zero problems whatsoever. None. At all.
But OK...this is Autopia, so:
The only rust converter I liked for this specific job has been off the market for years, so I no longer use that approach. Using rust-killer chemicals (acids/etc.) isn`t my approach either as it`s too hard to keep them off the surrounding paint (and IME the effective ones aren`t paint-friendly). So I too do it mechanically.
If you have a hand like a surgeon you can use a Dremel and the smallest engraving bit..
Use an illuminated and magnified viewing system and a tiny diamond burr and the process is downright Accumulator-proof. Somebody with better vision might not even need the viewing system, but I find it invaluable (I have a magnifying visor fitted with LEDs). A flexible extension shaft makes it easier to control, or at least more comfortable, but isn`t essential. I stick with 240grit burrs, but you do have to go slow and clean them frequently or they won`t last long.
Yeah, it can sound scary, but it isn`t all that hard if you think it through, use the right stuff, and approach it with the right mindset.
I prime with some "paint over rust" type product (NOT POR15!!) that`ll be OK as a primer (lots of considerations there...) and then touch up with whatever seems right for that job (DrColorChips, regular t/u paint, just depends).
One trick is to thin the paint and buy the finest tip brush you can find. Walmart has a decent set of fine tip brushes in their hobby/craft section.
I seldom go smaller than a 000/"3-Oh", especially with metallics.