The devil is in the detail
Indeed, it does seem that when it comes to details like connectors, the manufacturers tend to use the most expedient solution to hand rather than having the ideal custom made. I suppose this is because the market simply isn't big enough to warrant the cost in R&D on an individual level. I would have thought though that it was big enough for a connector manufacturer to invent something that could be sold to the market as a whole, also the reason why one of the biggest motor manufacturers, Bafang, haven't come up with a better solution, particularly for rear hub motors is a complete mystery.
I'd say that this was was the reasoning behind the version of the Pi with the centrally mounted motor (the nuvinci geared one), along with having all the electronics housed within the frame.