Right now, the minified files easily lead to conflicts when another PR with changes to the JS files has been merged. Can we improve this process?

My suggestion:

Remove minified files from develop and only generate and use them upon deploy to WordPress.org. This means we'd delete the minified files from the develop branch, change the SCRIPT_DEBUG if condition to add another constant and set this constant before deploying to .org.

e.g. $suffix = SCRIPT_DEBUG || ! GP_USE_MINIFIED ? '.css' : '.min.css';