Frustration is the worst user experience !
I find the doc straight forward, and don’t get much trouble to flash my keyboard without the Arduino IDE, so if the doc miss something, we must improve it 
If something goes bad here, please report it so it can be investigate (M1 Mac seems to reserve some surprises for users)
$ cd ${HOME}/git
$ git clone https://github.com/keyboardio/Kaleidoscope
$ cd ${HOME}/git/Kaleidoscope
$ make setup
$ export KALEIDOSCOPE_DIR=${HOME}/git/Kaleidoscope
$ cd examples/Devices/Keyboardio/Atreus
$ ### Edit the .ino files ###
$ make compile
$ make flash # Pressing the prog key
The missing part may be the need to reset the eeprom if Chrysalis was used to modify the layouts 
For the Chrysalis unfriendly experience, feel free to write a word about what you like/dislike, this may just be a Graphical VS. Cli way of life, but things can eventually be improved at a point 
Happy Hacking 
Romain