Are you using the Jetson nano development board? (https://developer.nvidia.com/embedded/jetson-nano-developer-kit). If so, then this board needs the SD card for storage and to boot. There is also a system on module board for the Jetson nano that has built in eMMC instead of using an SD card. However if you are using the regular dev board, then the SD card will be needed.
I’m not sure about the repo you linked. I’m guessing that this tool can be used to flash the eMMC of the system on module board, or it can flash the SD card on the dev board while its in the SD slot, instead of having to put the SD card in some sort of USB adapter.