I think too, I just reproduced!! Only by opening the wrong .editorproject file so I think these issues should not appear when using the editor in the good way.
Would be really happy to see the github repo! Once done and working with the required changes etc. it must be included in the documentation on doc.babylonjs.com. I tested on my side and it works using the right buttons at the right moments (that must be explained better in the documentation then).
I’m polishing the release 3.1.2 and then will focus on improving the workflow according to this discussion 
For the SceneLoader, after loading the .babylon file, the example loads in fact the metadatas file (and not the editor’s project file). This file contains only the added value of the editor (custom post-processes, scripts, graphs, etc.). Then, the example calls .ApplyExtensions according to the loaded metadatas to create the custom post-processes etc. The RootUrl property is set to provide the extensions (while being applied) the information that the scene’s assets are located in this folder (here ./scene/) because the extensions can request files themself (like textures, sounds etc.).
I think the RootUrl property can be passed to the .ApplyExtensions function like this to save a line:
// Apply extensions (such as custom code, custom materials etc.)
Extensions.ApplyExtensions(this.scene, JSON.parse(data), ‘./scene/’);