It is quite understandable that such an utterance sometimes causes confusion, but the confusion has more to do with social conventions than with English language. So far as the language goes, the phrase indeed means what it seems to mean, which implies a realistic possibility that things will change in the future (leaving it vague how far in the future that may be, although the context will usually provide some clues about that). In other words it would be misleading to say ‘not for now’, if what’s on one’s mind is ‘never’. However, people sometimes, to soften the blow of the rejection, or to avoid confrontation, do say ‘not for now’, while thinking ‘never’. That may be a problem, but it is a problem outside the scope of ELU StackExchange.
Incidentally, the phrases 'at this time' and ‘at present’, are sometimes used in the same way: an inquiry from a customer to a business about whether some service is available often produces a response that it is not available ‘at this time’, even though the business doesn’t have the slightest intention of making it available at some other time.