I recently read a plausible reason that I hadn’t thought of yet:

Apple would need to include a specific flexible cable rated for continuous movement with the mouse. If the port was in the regular spot, then people would ofc also use it wired at times. However if buyers would use regular charging cables, then the experience would both be worse and the cables might get damaged over time from bending.

I still think the main reason is simply that they value form over function, otherwise the shape would be more ergonomic, but it’s another interesting factor to consider.