It’s all about tension on the lightning connector imo - the connector isn’t designed for that level of flexibility, so it would break and it’s not like they’re going to use a different connector just for the mouse
This is the best steelmanning I've seen of the Magic Mouse charging port design; I'm surprised I never encountered it before. It actually makes a lot of sense considering how stiff the cables typically are, and it also then makes sense that the (immobile) Magic Keyboard and Magic Trackpad do have a charging port you can use while the device is in use.
It's nonsense -- plenty of people use phones and iPads while tethered to a charging cord. The port is well secured to the logic board of the device because it has to survive a lot of yanking, accidental falls, etc. It doesn't explain the Magic Mouse design.