I suppose that color palette is used to limit amount of memory used and be able to speed up layers drawing on screens.
a dedicated alpha channel for transparency means 25% more data and more computation time also.
A dedicated color to do so was an easy way to skip pixel drawing, and also an easy way to edit sprites.
Ok, nowadays those arguments do not count anymore. We got Terabyte storage, Gigabyte of memory and Ghz of cpu clock ...
Moreover, we got dedicated hardware (graphic cards) optimized for this computation