@tamalock

I just spent hours trying to figure out the chain of config files, overloads and automatic overwritings happening and I don't feel like I'm any closer to understanding the mess.

You need to read the documentation:

https://recalbox.gitbook.io/documentation/advanced-user/configuration/configuration-overload https://recalbox.gitbook.io/documentation/advanced-user/configuration/configuration-overload/retroarch-overloads

let's say I want to set input_menu_toggle_btn to 10 for ALL cores loaded through Retroarch - how do I get Recalbox to set that automatically when it does its overwrite of retroarchcustom.cfg?

Path: /recalbox/share/roms/.retroarch.cfg

With the text:

input_menu_toggle_btn=10