Linux itself, and the Ubuntu distribution, are all public domain software. NVIDIA makes the driver install step a separate step without mixing the two (this means you are the one installing it, not NVIDIA). This means a second step to install the NVIDIA-specific software is required. This installs the video/GPU driver (and others…this is significant in your case because video driver install is required to go to graphical mode).
If you were to flash a new version of L4T (“Linux for Tegra” is what the Ubuntu is called after you overlay the NVIDIA drivers on top of it…but really it is just Ubuntu), then the unpacking of the sample rootfs unpacks an entirely public domain Ubuntu, and the apply_binaries.sh step is what does exactly what your above command would do…but it does it prior to flashing instead of after flashing.
You might run the command just to see it. If you flash it erases everything anyway…there is no harm. You could actually run that command multiple times and the result would be the same. If some package overwrote a video driver by accident, then running this command would fix it (or the equivalent of this command).
Newer releases of the L4T on the TX1 are far superior to the original release it ships with in many ways. You’ll want to flash it anyway.
JetPack on your host will do a lot of the work for you, and then offer to install additional packages to both host and Jetson. So far as flash goes though, JetPack is a front end to the command line flash…flashing by command line is no different than flashing by JetPack (other than JetPack doing downloads for you and implying you don’t need to know the command line flash details).
If you flash on command line you can use any Linux x86_64 PC host plus the micro-B USB cable provided. If you use JetPack you are required to have a host with Ubuntu 14.04 or 16.04. Host side package install further requires the host to have a compatible NVIDIA video card. Extra package installs require a wired ethernet cable to the Jetson (host can have WiFi to the internet). Package installs can run at any later time…JetPack does not have to flash.
FYI, currently R28.1 is the most recent L4T release of a TX1. This is via JetPack3.1 if you desire, otherwise it is the driver package plus sample rootfs to download. There is a JetPack3.2 which is a testing pre-release, but this does not cover a TX1. Here is the R28.1 downloads page (there is a JetPack link at the top as well):