It seems to me Protopie has been designed to support developing pies containing a maximum of 5-6 scenes because more than 6 scenes make it quite complex and it slows down the performance. Perhaps, Protopie team should change the definition of Scenes and Artboard and make it similar to Sketch or Adobe XD.
Scenes should mean a part of the user journey while artboards are a subset of scenes. For example, if we have to create a high-fidelity Instagram prototype, the following will be scenes and artboards:
Registration/Login (containing 12 artboards)
User profile (containing 5 artboards)
Uploading new photos (containing 5 artboards)
and also giving an option to create links between scenes and artboards.
For a visual demo, I am attaching a demo of how I visualize the better scene and artboard management (inspired by Sketch)
I have shared this feature post on Protopie facebook group and it has gathered a lot of reactions from Protopie users: