Is the motor chinese bafang motor? I thought they did internal development with Williaams F1?
At the end of the day, it all about the ride. With such a small wheel, I doubt that the CG will be that much higher than if placed at bb. I have never ridden the e-brompton, so I have no idea how it rides. But with the motor config on front wheel, I think its possible to swap out the wheel and put a normal wheel so you can still use it like a normal brompton. Don't know whether you can take out the battery and used the bag for groceries though.
To do motor at bb, will mean a totally new and different bike. (Like Bosch config.) Just imagine the domino effects of trying to keep track of inventory, spare parts etc.