Yeah since making this post I've learned a lot about factorio modding and the lua API. Currently have working mod settings that influence world generation, the UX is not as bad as I though it would be this way.

Sadly there is no way to disable the automatic map generation (even on a new LuaSurface ...

Thank you, I was pretty sure that would be the case and it's good to have confirmation - I suppose I'll work around it with mod settings.

I'm interested in writing a mod which expands the available "Map Generator" settings (by adding new settings and extending existing ones). However, have so far proven unsuccessful at finding any method of implementing this on the actual generator UI (it looks as though additional presets are easy to ...