The idea is the user edits the collision polygon visually in the Animations Editor. Why do you want to overwrite it? Do you expect it to work with undo? Changing the project from addons is quite tricky - just undo alone is quite a complicated area: either we add all the (significant) API surface to handle undo and redo properly, and you write all the code necessary to handle it for your changes, or we don't and in some cases undo is broken for the user.