I've worked with a company doing this - and it did work. It was a real b*tch to get going. I hope I am never involved in another such deployment.
I think you need to make sure your AD Sync has device write back configured, so AADJ machines also appear in your local Active Directory. The certificates get issued against those.
Good luck. I think it took 3 weeks to get going. Then after 12 months a certificate expired, somewhere, and it took another three weeks to fix. I'm not looking forward to next year ...