They added the connector for the same reason that they connected i2s lines between the CPU and the bluetooth chip, despite that this interface also doesn’t work right – because it can be MADE to work right (which I have accomplished for the i2s), the issue is software.
As to why they can’t make the board a few mm bigger, it is because if they did, it would no longer adhere to the 96boards consumer specifications. That connector is not a 96boards requirement, but the physical dimensions of the board are.
It could also be argued that it could be more practical in some instances to have the connected devices sticking out the side of the board than standing over the board. Consider for a moment, putting the board in an enclosure. To make it possible to snap a board onto the connector with it sticking out sideways doesn’t require as much of the board exposed (for fingers to touch) as it would if the connector pointed inward.