I just remembered my sysnand is on FW 11.0 and that was the last time my gamecart slot firmware was updated. When installing an original gamecart on 17.01 emunand the switch would crash. As a fix for those that have the same issue, make sure in the Atmosphere/config folder that you have stratosphere.ini file with this line: nogc = 0
That will stop the crash when you reboot and you have a gamecart in the slot during boot, or stop it crashing when you insert a gamecart after booting.
As for dumping with nxdumptool from the release link, I still had to dump all the files individually with a few button presses, it would be good if there was an option to dump all these with a single click with the correct options enabled. Maybe this can done pretty easily with modded source code as it shouldn't be too hard to do.