I believe that they do that for expediency's sake. On MP5's they add an extension to reroute the wiring to the front and a large connector on the rear would be too big. On an M4/M16...same thing re. space available if they want to run a collapsible stock. Same on an AK...small connector fits through the receiver to the stock easier.
For all of those...all they need is a bucket of small to large extensions and they're ready to knock out which ever model they need. Faster to do it easy than to do it right (i.e. no intermediate connector...straight wired).
Large batteries have large connectors for a reason. Sticking a small connector in there defeats the purpose.
But again...you don't have to change it...it just works everything harder and robs performance.