Jetsons don’t work like a regular computer. There is no BIOS, but you still have to have the equivalent in software. It is the BIOS that makes so much of it standard. When you flash a Jetson you are more or less also doing the equivalent of flashing the CMOS/BIOS. The different models of Jetsons also have some differences.
I don’t know if you have the AGX Orin “developer kit” sold by NVIDIA, or if it is instead an AGX module on a third party carrier board, but either way, this would have eMMC memory. The boot software is designed to try to create a UEFI boot environment, but this isn’t complete in JetPack 5.x. Even though UEFI is complete in JetPack 6.x, there are still some of the same details to consider.
The bootloader does not start until after the boot software reaches a certain stage, and both the early boot software and the bootloader could be considered their own micro operating systems on bare metal. The earliest stages need to know details of the exact hardware and will be very specific code for the exact hardware. This creates the UEFI abstraction, which is when there is some generic nature to this. Even so, UEFI then loads the bootloader, which is also its own operating system. The bootloader thus needs drivers for everything required during boot, and for anything that must be set up for the Linux kernel when it starts. This includes drivers for any storage device used.
The default for the AGX Orin will be drivers for the eMMC, but not for the SD card. One can choose flash options for external media, but these more or less depend on an initrd which serves as an adapter for bootloader requirements to Linux requirements. Your Linux might understand the SD card slot on the carrier board, but it doesn’t mean the bootloader will understand this. On the purely SD card models (without eMMC) there is QSPI memory on the module used for that content, including the SD card driver during boot stages. The eMMC models lack the direct availability of SD card booting.
You must essentially flash with some external media options in order to get an eMMC model to boot from SD card (or from any external media). During flash the Jetson becomes a custom USB device and is not a mass storage device; the driver for this custom device lives on the host PC, and that driver is a binary executable for desktop PC architecture under a Linux operating system. Without recovery mode you cannot alter the software at those lower levels (at least not without a large amount of detailed knowledge, and in that case, you’d still need a Linux host PC to create some of the content).
There are upgrade paths in some cases, but considering you are going from one model of boot to eMMC to a different model on external media, there isn’t much you can do other than use an external host PC running Linux. Networking does not exist during the process (yes, flash completes, and then the Jetson boots with networking, but this is after flash).