Since it depends on how the equipment handles the processing of continuous tone and linework theres no single answer to that. Newer equipment seems to be getting away from the "dual-level" processing (I haven't seen this problem on output in a few years, but that doesn't mean it isn't still out there in some shops).
If the printer can handle the live transparency, that's a good sign, and you should send a PDF that is not flattened.
