Ross,
The way we do it on the new vehicles is, sand down, grind clean (emphasize: CLEAN) for bondo, but over top of paint is fine for putty.
After you have the body work done, then comes a coat of etch primer (or metal prep..basically same). Then comes a couple coats of fill primer.
Sand, any spots that reached bare metal get a spray of etch primer (out of a rattle can). Then paint.
I'd say if your doing all this, why not strive to make it perfect. Skipping steps means regret later and more $$$.
Also, as long as its inside in a building with a relatively stable temp, bare metal is fine.
Good Luck
