The charging port on the bottom has never bothered me. I enjoy the mouse every day. After all, 90% of the mouse's life (when I use this mouse) I prefer the touch surface without
notch, so this compromise not only looks aesthetically but also functionally well balanced. How would you have done it better? I'd be really interested to know. Maybe draw it and post it in here.
Since there are a lot of people here at MacRumors who like to park charging mats for all products on the table, they might be happy to have a soft mattress gimmick for their mouse to rest on while lying on its back.
On the other hand, Apple has used a hard plastic for the sensitive surface that normally does not scratch.