I have a custom board. And I have already successfully flashed my jetson in runtime mode.
We also managed to install all the software through the SDK manager.
If your custom board does not have significant design as devkit, you could use SDK Manager to flash the board.
If you have some differences related to the custom carrier board, you might need to modify pinmux/device tree or something else and create your own board config for flash script to flash your board.