There's Samurai Gunn 2, and Samurai Gunn 2 rework, where the internals got completely remade from the ground up.
Yes, pre rework, the game had a "setdress editor" where you could, in this same way, place sections of sprites to create a level. The collision and entities were not editable this way though, they were part of the gamemaker level file and required other tools to edit.
Post rework the built in setdress editor is gone, but now all entities and colliders are packaged along with the sprites in a single JSON file, making it a lot more feasible to make my own editor, and have the whole thing be a complete experience.
Yes the developers have their own internal tools, but I don't think there's literally any info on how they look or behave and they are not public. Most likely the dev tools are just not user friendly, it would just take time away from the game to do so, and they are also probably closely integrated into the game itself, making it hard to release? I dont know.