It's a red herring argument. The only difference between iPhones with the secure enclave and those without is that the SE has it's own SW update process giving extra security to the code (and thus the keys) inside it. In this particular case (dead terrorist's phone) the lack of SE means Apple can update all the flash containing the OS plus the code to decrypt the AES key in one update. With SE it would require two updates. It slightly eases one difficulty but doesn't change the fact that the FBI is demanding an entirely new function.
That function is a passcode tester that allows testing through a new channel. Currently all passcode entry is via the on-screen keyboard. The FBI demands a new channel through USB, bluetooth or wifi. The SE or lack thereof is not involved with that new functionality. That new functionality, in conjunction with turning off the attempt count and turning off the auto-erase constitutes a back door.
The diagram showing the secure enclave categorizes the kernel as firmware, the diagram without the secure enclave categorizes the kernel not as firmware but as software. Also, in the diagram showing the secure enclave the user partition is encrypted, in the other diagram it is not. These likely bear on the difficulty of any modifications.