I recently installed a square taper crankset and cartridge BB on a steel frame that previously had an external bearing system (long story). Because the BB shell had been faced, the paint covering the faces is gone and the steel is exposed. The faces are still very clean. Apparently having the BB cups pressed up against the shell with a little grease inbetween was enough to stave off corrosion for the last 2 years or so.

My only worry is that when the new bottom bracket (Shimano UN53) was installed and torqued down, i noticed that the flange on the plastic NDS cup did not make full contact with the shell, so there's a tiny air gap (maybe 0.5mm) where water and salt can get in and attack the unprotected metal. Should I be concerned about this, and if so, what is the best way to protect the shell? Would removing the NDS cup and applying a couple of coats of touch-up paint do the job, or is it not worth worrying about? I'd have to scrape the paint off if I ever wanted to use an external BB again but at least I wouldn't have to remove any more metal.

Smear a little car wax onto the surface. It will attract less dirt than grease. Any wax will do, even furniture polish.

Not worth worrying about, but you can take off the cup and paint it if you want. Unlike the inside of a chainstay or main tube, the metal there is very thick and will not rust away to nothing. You might get some surface rust on the face but it won't spread, in my experience.

I always put a goodly amount of Tef-Gel TEF-GEL - Ultra safety systems - Home page on all dissimilar metal joints. It is specifically designed to prevent electrolytic corrosion and seizing between dissimilar metal surfaces in marine applications, which is about as tough service as it gets.

Paint..