I understand Sam's point, separating the code from the layout.
But, I would like the ability to change themes without having to redo my changes. I think a developer should be able to switch to a new theme with minimal amount of work.
So, I support Ingo's idea that it should be up to the developer. Can you add a feature that allows site developers to choose how things are overriden? Or, as Ingo mentioned, mysite templates are given priority?