Think I've found a decent Minetest workflow for the tiny games I want to build.
- Add SpawnBuilder and Modgen to a vanilla game.
- Create a custom mod for game specific stuff.
- Build the setting in the generated world.
- Export the setting with Modgen.
- Copy vanilla Minetest removing unused mods and adding metadata.
- Copy the Modgen export into the custom game together with the custom mod.
- Test and revise.