Me, @waxen anvil, @humble chasm and a few other people have built a mod loader that is being currently used in:
- Brotato
- Dome Keeper
- Endoparasitic
- More to come
It's fully open source, with easy setup and has steam workshop support.
It would be great to have this game added onto the current list. Here is a link to the repository: https://github.com/GodotModding/godot-mod-loader