First, check that the
/boot/config.txt you are editing is actually the on the first partition of the SD card. Although it is not technically necessary, Raspbian is set up to mount this partition on
/boot automatically, so online tutorials will refer to it that way -- and
raspi-config, used in the Adafruit guide, presumes this is the case.
However, if the file doesn't exist it will be created, and if Kali doesn't use the scheme Raspbian does (comments here imply that), this means it will just create a file in the otherwise empty
/boot directory, which won't actually be used when the system boots. The Pi makes use of a vfat formatted partition at the beginning of the SD card, where firmware and bootloader must be located (and generally also the kernel). You can set things up the same way by adding the following line to
/dev/mmcblk0p1 /boot vfat defaults 0 2
Note this will render anything actually in that directory inaccessible (but not delete it) although from the sounds of things there was nothing there to start with.
In any case, the contents of that partition --
/dev/mmcblk0p1 -- should resemble this -- and it must be there or the Pi would not work. That github repo actually doesn't contain a
config.txt, but whether or not there's one there on your system, that partition is where you want to apply it. If you mount this before running
raspi-config it should work out. If you don't want it in
mount -t vfat /dev/mmcblk0p1 /boot
This may be an issue. It predates the release of the Pi 3 and may never have been updated for it. Further, there is a Pi 3 specific device tree overlay in
/boot and this implies you don't have that either.
You need to replace the contents of the
/boot partition referred to above with this and copy the
-v7+ modules directory from here into
/lib/modules. It must remain named exactly the same.