The bottom is the best place for it. It would look really bad on the top and the rest of the mouse is kinda thin.
Also the port is a retrofit over the previous model which took a pair of AA batteries.
It’s not some terrible design choice from Apple, it’s a lazy revision to an old removable battery mouse without much effort needed to update the plastic tooling to make it.
And the rest of the industry (which is basically Logitech, let's face it) isn't in a race to the bottom to make things thinner and thinner each year.
Apple isn't doing that so much now, maybe they can make a good mouse again with a port that lets it work as both a wired and wireless device. The way the Magic Trackpad does it is very nice.
Also the port is a retrofit over the previous model which took a pair of AA batteries.
It’s not some terrible design choice from Apple, it’s a lazy revision to an old removable battery mouse without much effort needed to update the plastic tooling to make it.