I think you can move the collision shapes within an Area, though I have not tested myself. I know that collision shapes can have translation, rotation, and scale offsets when compared to parent nodes. The scale is tricky though and should, probably, be avoided, especially if the scaling is not uniform. I’ve had several issues with 3D collision shapes due to non-uniform scales.
I suppose the best way to know would be to test and see what happens. There might be a small delay before the Area notices the changes though, which may be problematic.