When your threat model is "someone on the network intercepting messages", it doesn't matter if you control the hardware. When your threat model is "someone owns my device", it still doesn't matter if you control the hardware, because, in that scenario, Apple is the bad actor you're trying to protect against.

There's no scenario where a third party has compromised your phone without Apple's collaboration, which is the only scenario where the secure enclave would maybe protect you (and even then, the bad actor would just read your messages off the screen or memory directly).