Difference between CSGBox3D and MeshInstance3D

[simple smelt]

CSGBoxes give you a mesh that is more easily editable through the editor and so it's nice for designing levels. It costs more performance in the end - however you could write a script or use a plugin to convert your CSGBoxes into MeshInstance3Ds.

https://github.com/StrayEddy/GodotPlugin-CSGToMeshInstance
Here's one that lets you do it selectively as needed