I like to use OBJs, and it'd be very useful if there was a way to write back to the OBJ file to avoid duplicated mesh files. Godot supports the ability for OBJ files to have vertex colors via an extension. It's so much easier to use this plugin than to do this stuff in blender.

I have 2 (or maybe 3) good news for you :)

1. Export OBJ and GLTF is coming to Vertex Studio Godot
2. Vertex Studio is also coming for Blender (and it works in Object and Edit mode, so you can paint/manage vertices and normals using all the cool tools from Vertex Studio)