Turns out that the Pi display has a better viewing angle from one direction than the other. The Pi Foundation flipped the display to account for this, assuming that the user would be looking down on the display from above.
In my case I think the user will be looking from 'below', so turning the display over makes sense. Which means I don't have to lengthen the jumper wires, but I do need to make some modifications to the mounting hole positions and screen cutout.
More info and software fix: