This is just some background which you might find useful.
The “Linux_for_Tegra/” directory would be on a host PC when flashing via an Ubuntu host, and is not on the SD card itself. There is a subdirectory, “Linux_for_Tegra/rootfs/”, which along with Jetson model and carrier board model, is used to create images. The SD card image is just one possible image, and is prebuilt, whereas the host PC can do a lot more.
Jetsons do not have a hardware BIOS the way you might think of most computers. Jetsons do have the equivalent in software. During a “full” flash of a Jetson you are more or less also flashing BIOS (not really a BIOS, just binary data), the bootloader, and the o/s. A true BIOS allows a system to “self flash”, e.g., putting an install disk in a slot and running it. Jetsons can’t do that.
L4T (“Linux for Tegra”) is just what Ubuntu is called after adding the NVIDIA driver content for use with a Jetson. A list of L4T releases and compatibility is here:
https://developer.nvidia.com/linux-tegra
Each release has a major release version, e.g., L4T R36.x, and a given “host PC” JetPack release tends to target installing that L4T release (there are other JetPack packages, but we’re talking about the flash software on the host PC side during flash; JetPack in this case can flash earlier L4T releases, but won’t show those unless it is started with the option to show earlier releases). In the case of a prebuilt SD card image it is necessary that the Jetson already have the “equivalent to a BIOS” software already installed on the module itself for that major version. For example, L4T 35.x can use any L4T R35.x SD card image; any L4T R36.x prebuilt image can work with a Jetson that has the rest of the software for L4T R36.x. The software-based content for loading the o/s must be in place because it isn’t a generalized BIOS. To change major release you must flash the actual Jetson, and this is different than flashing an SD card.
To emphasize, JetPack is not installed on the SD card, it is L4T installed there. There may be a package you run into called JetPack, but it isn’t the o/s itself.
When you’ve reached the stage that you set up a user name and password it implies your SD card worked for what is on the Jetson itself. This is first boot setup (you can’t use default name and password anymore if you want to sell your product in California). You won’t have to flash the actual Jetson for that major release of L4T. Any package install from the Jetson will be quite different than the package on a host PC used for full flash. Whenever you ask about installing a package be sure to mention it is on the Jetson or on the host PC.
I don’t know what all of the available packages are when installed from the Jetson itself, but the main package to install on a host PC for full flash is JetPack (SDK Manager is just a smart network layer on top of the JetPack GUI, so they come together). JetPack in that case is just a GUI to flashing software, and the actual flash software behind JetPack/SDK Manager is called the “driver package”. A Jetson in recovery mode is a custom USB device which the driver package understands, and the driver package is installed on the host PC.
The real question is “what do you want installed?”. Once you’ve logged in to the Jetson itself there are a number of things you can do for additional software.