We encountered similar issues with SCEP certificates and Autopilot pre-provisioning with Entra hybrid joined devices. During provisioning phase, the computer object gets created with ODJ, but the device only gets a certificate without AD object SID in SAN URI even if the SCEP certificate profile includes the configuration. The device thus cannot establishish a connection/trust relationship to AD through Microsoft NPS because of 802.1X certificate strong mapping requirement and it has no SID which is required for Intune strong mapping enabled SCEP certificate deployment.
I do know that Entra hybrid join requirements for Autopilot deployment state that the device must have "access to an Active Directory domain controller of the domain being joined", but this was never an issue using 802.1X EAP-TLS before strong mapping enforcement AFAIK. At the moment, compatibility mode seems to be the only way to resolve this temporarily until September 2025.
Interested to hear, if you get some resolution for the issues from MS support.