Hello timmakestuff, the Godot folder contains a Godot project that you can open directly in Godot to start using, or copy into your existing project.
The zip folder includes all versions: RPG Maker, Unity, Godot, GameMaker, etc... which is why it is larger.
Note: If you plan to copy the files into your project, please remember to create a backup first. Always be cautious when doing so.