I’m not sure what changes are in place for SDK Manager (I won’t be able to get to it till this weekend), but JetPack is the intermediate software. Somewhere during the install it should ask which method to use, e.g., ethernet over USB, direct ethernet with host as router, or to a router appliance. This is what picks the method.
The presence of the ip-over-usb is in part coincidental as an example of setting up Linux “gadget” mode USB. Regardless of the interface, should you give it the IP address, and if from your host you can connect via “ssh nvidia@”, then it will work. The various options determine whether the host itself will be altered to act as a router or not…the actual communications will be the same once the Xavier has an IP address.
FYI, you can skip flash and run package install at any time, but you’ll probably need to manually enter the IP address when doing so.