The "Bondo Glazing & Spot Putty" is designed for filling pin-holes in Bondo and body filler and stuff like that, so I think it'd be exactly what you're looking for. And it should be able to take any kind of paint you can throw at it.
That's what I use for small jobs like minor seam filling. Available at almost any auto parts store and not too expensive. And, yes, it takes primer and paint very well. It also sands nicely, making it easy to blend in with the surrounding material.
It does have some cons though. It has a relatively short working time, a minor amount of shrinkage (not noticeable in small quantities), it's not particularly durable if you plan to use it to add thin surface detail (i.e., it breaks easily), and if used in large quantities it can melt thin styrene as it cures.
For large gaps and/or adding sculpted surface detail I prefer Aves Apoxie Sculpt, a two-part epoxy-like putty. It's more difficult to obtain and it takes a little getting used to, but it sculpts easily, can be thinned or smoothed with water, and has a 2-3 hour working time (allegedly--I find it starts curing within 45-60 minutes).
Aves Apoxie Sculpt also has some cons. It takes 24 hours to cure completely (i.e., before you can drill, grind, carve, etc.) and, in my experience, is usually harder than most styrenes and resins when fully cured, which can sometimes make sanding/blending difficult.
That said, I find these two products to be easier to work with and better than most other spot and two-part putties.