I don't think there's anything cryptographic about the baseband communication on an iPhone, or that they're connected through the Secure Enclave. I think they're just PCIe endpoints with IOMMU (which is fine as long as the IOMMU is configured correctly). My understanding is that for most iPhones, a repair shop can replace the baseband hardware itself without the phone noticing, which also suggests that there's no pairing or hardware trust model / key exchange between the AP and baseband.

Post-boot communication with the host processor on Qualcomm-baseband iPhones (iPhone 12-16 non-E) is the usual Qualcomm QMI/QMUX over PCIe (CommCenter uses libPCITransport to send messages).

The Platform Security document just says "On devices with cellular access, a cellular baseband subsystem performs additional secure booting using signed software and keys verified by the baseband processor" and "Each network processor is on its own isolated PCIe bus. An Input/ Output Memory Management Unit (IOMMU) on each PCIe bus further limits the network processor’s DMA access to only memory and resources containing its network packets and control structures."