Nobody's responding to this, so I'll take a crack at it.
From what I can tell, you can create everything that you could create with the Godot GUI completely in code, so you wouldn't have an issue with the idea of creating things on the fly from scripts. That's going to be a bit difficult, I'd say, but it's possible.
Now as for modding, it should be possible to load external scripts using the standard script loading procedure, just with the current working directory or the user's directory ("user://") instead of the resource directory ("res://"). I think the best course of action is to try out a simple test, where you create a game that runs from an empty directory, and create a GDScript file that does something simple. That way, you can test it out and see how it works.
I'd understand if there aren't any tutorials; modding is pretty unusual, even for today's indie games. However, there are results if you search for Godot modding; for example, here's a short post on the Q&A forum. As mentioned in that post, security should be a top concern to ensure that modding support doesn't become a virus or malware transport vector. That might be possible to guard against from your side programmatically, but it's something to be aware of and do tests on, just to be sure.
