I tried this again last night, spent a bunch of time remapping my buttons for the controller, and then realized when I tried to start the game that the prompts did not update and it was kind of a mix of what I set and what the defaults were, which they do not seem to surface the default mappings for a controller. So I figured I would just set it back to default, but sure enough, it wouldn’t stick no matter what I did. After a bit of googling it appears that I need to manually delete my settings.ini file, and go through a couple more hoops to get it to work.
I guess this is what I get for trying to play an early access game, on a mac dual-boot, with a controller. I should really just learn my lesson what wait for Xbox. Damn you streamers/posters!