I'm not claiming it is in ROM or that it is not upgradeable if you are Apple and have physical access to the device. I'm not sure on that point. What I think must be the case is that Apple can't remotely upgrade the SE firmware as part of its iOS update mechanism. Although, to be perfectly honest, I have not seen this explicitly documented.
So... it sounds like you more or less agree with me. Apple can comply with this court order and open your secure device. We just differ as to whether they can do it over the air.
(FWIW: OTA firmware updates are routine in the industry. I've worked on such systems professionally, though not for Apple.)