I can confirm that we’re looking at refining this versioning system, because I agree that this is a workflow that makes it a little too easy to shoot yourself in the foot 
I think the particular feature you’re describing could also lead to unpleasant surprises, though - I want my app to behave the same in dev and published modes, so I can debug it in the editor! Automatically switching which dependency version we use would be rather unhelpful.
Our current thoughts envision more complex versioning schemes, which would allow you to track more than just “development” or “production”. This would allow (eg) dependencies with a “v1” and a “v2” API, without creating separate dependency apps. We’ll keep you posted!