While the exact reason has never been documented, if you look at that mouse's design, you'll see that its first generation had a regular battery compartment on the bottom. When gen 2 arrived, they fully reused the same shell and only replaced that bottom part to now be an integrated battery with a charging port instead of a compartment for AAs. Moving the charging port would've required a brand new design, since every edge of the mouse tapers way too much for a port to be placed anywhere else. They would also probably need to change more of the internal structure, as opposed to just swapping a battery module and changing the bottom lid. In this case the constraint seems to just be about functionality and manufacturing. Apple has made many controversial design decisions that have no functional justifications in the past, yet people keep bringing up the mouse.