Yes, we use both phrases, and I'd understand them to mean the same. The second is more unusual, but it certainly makes sense in the context.
In fact, I don't think that a native speaker would be likely to say 'He photographs well' to mean that he is good at taking photos. A foreign learner might use this phrase to mean that, but it might sound unnatural coming from a native speaker.
Another natural-sounding phrase (which IS ambiguous) is 'He takes a good photograph'. If it's clear from the context, this can also mean that he looks good in photographs. This phrase and 'He photographs well' are both nice examples of ergative verbs, if anyone is interested.