Hello!
To configure the pinmux you should use the pinmux spreadsheet for TX2 [0] and then convert the generate DTSI files into the MB1 files as described here [1].
The kernel image and DTB can be loaded from the rootfs via the /boot/extlinux/extlinux.conf file. By default the kernel image is loaded from /boot/Image but the DTB is still loaded from flash. So unless you update the extlinux.conf to load the DTB from the rootfs, you still need to flash it.
Regards,
Jon
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[1] Where To Put Pinmux Spreadsheet DTSI Files