Everything you're talking about can be done - to some extent. But these processes all have their limitations. Yes, you can scan sculptures and print them out. But just as you've noticed with your molds, the scans won't necessarily be perfect, and the prints might have artifacts of the process you'll need to remedy somehow.

Without seeing the specific trinket boxes you refer to, it's hard to say how well they'd scan. But they sound like something that might best be constructed from scratch in a CAD modeling program.

There are many different 3D printing processes, so one can't generalize too much, but most kinds of 3D prints can be painted.

Andrew Werby
www.computersculpture.com