Godot can load data through internet through HTTPClient: docs.godotengine.org/en/stable/classes/class_httpclient.html
I suppose you can share resources pack on some site and let users set resource loading URL in the game. This way that they can download your pack, modify resources and then upload it somewhere and set the game load resources from that new URL.
Seems like a far way around, but think of the good side: it would be easy for users to share they mods. And you can even make a workshop for a central exchange point.