Moderators and other well-meaning users often comment if they think a post can be improved. If the poster then takes the advice and makes the suggested edit, is it appropriate for the poster to then flag the helpful comment as obsolete? It seems that it should be, my question is more about etiquette than anything else.
I would recommend not immediately flagging the comment as obsolete.
Edits can be reverted, or obliterated in successive edits. There might be answers to the question that refer to an earlier formulation. Or there might be a chain of comments that relate to each other, and deleting one will render the dialogue nonsensical.
Until the Q&A has "stabilized", you can't be sure that the comments have no value. My rule of thumb is that if the question hasn't had much activity for a week or so, it's safe to delete (or flag) obsolete comments.