I wanted to flag a mod, but I realized that the mod itself would mark it as a not useful flag. How can I flag a mod?
Actually if a moderator receives a flag on their own post, they ask one of their fellow moderators to intervene. You can't be an impartial judge for a flag on your own post. But I understand the point you're making: that a moderator does indeed have the ability to dismiss flags on their own posts, even though our policy isn't to do so.
If you have a concern about a specific action taken by a moderator, you can do one of two things:
Make a post on meta about what happened, and let the community weigh in with their thoughts on the matter. Maybe a mistake was made that we need to rectify. Maybe we're handling something in a way the community disagrees with in general. Maybe a change in policy needs to be made. Maybe you're misunderstanding something/the community doesn't agree with your viewpoint. You don't know until you ask the community on meta, so this could resolve your issue.
If you feel the matter would better be discussed in private and doesn't affect the community as a whole, you can contact the Stack Exchange staff about a moderator on the Contact Us page. You can address all your concerns there privately, SE staff will reply to you, and if they feel the matter is something they need to correct a moderator on, they will bring the matter to our attention.
I hope this answers your concerns; please feel free to ask for clarification if you feel it's required.