Is Cleidocranial Dysplasia an automatic DQ in MEPS?

Only one way to be 100% about it and that is to go and see. MEPS is not going to cost you anything except your time. If you are worried about your weight, your recruiter can help you with that (or just start walking and running every day. That alone can help a lot).
If you have a thick neck to go along with your huge head, that can help a lot if you have to be taped for body fat.
Also, keep in mind if one branch can't/won't accept you, that does not immediately DQ you from another branch.

Do some upfront work and Google disqualifying medical conditions for military. I took a peek, and those keywords are not listed. So if the MEPS Doc says it's a disqualification, ask for the specific reference. They can have pretty big egos and don't like to be challenged, but you have nothing to lose. If the Doc does put down a disqualifying condition you don't have, then his license/contract is being risked. Sometimes in a downsizing or more people interested than needed situations, the MEPS Docs are "encouraged" to lean towards the cream of the crop. Hopefully, you'll just get a straight shooter. The other thing is to make sure you do real well on the testing aspects, lest you encourage them to find a reason to toss. BTW, body shapes which scream the tape test won't give a decent answer begs for the dunk test. Just be ready for that. If you get in and progress, do well so you don't encourage a test that may be problematical. Make sure you look at the long game. BTW, I had a Samoan Master Chief who looked like a brick outhouse. They dunked him once early in his career. He walked around the deep end for a while before deciding to come up. They never had to cajones to demand that again.