64G AGX Orin boot Order Getting Reset (JetPack 5.1.1 - L4T r35.3.1)

Do you mean that you would unplug the NVMe when it gets hot?

As I state before, UEFI would add the new device to the Top in boot-order.
In your case, you could refer to the following stepw to configure it to the Bottom

UEFI menu → Device Manager → NVIDIA Configuration → Boot Configuration → Add new devices to top or bottom of boot order → Bottom