It is a useful tool so well worth the five minutes to setup - you’ve linked to the v2 CLI, this is the one you want: https://www.thethingsindustries.com/docs/the-things-stack/interact/cli/ and I find this helps navigating the options: http://descartes.co.uk/TTSv3CLI.html
Microchip are pretty through so I suggest you are over-thinking - I’d not tried my SAMR34 board on ABP on v3 but all I did was setup a device on my test application, put the keys in to the right places and bingo. Let me see if I can fake an AU combo.