Have an A1 upper that is already cerakoted, tried using the dark park alumahyde over it. Sprayed that and a anodized lower at the same time, same cure time and coats but the upper started bubbling and peeling like it never fully cured.

Both parts we're thoroughly degreased and prepped the same, the lowers finish seems to be rock hard.

Is the Cerakote just too smooth for good adhesion?

Is bead blasting off the Cerakote my only option?

You answered your own question, blast it and try again.