I can’t speak for Apple’s design process, but for me, I’ve thought of and seen some personal projects use PCIe connectors because they’re cheap and have dozens of connections. I even saw a teardown on EEVBlog a while back of a piece of test equipment that used PCIe connectors for board-to-board interconnects.

For $2 or so in quantity 1, I can order an x16 connector from DigiKey and have 164 pins to connect two modules together. And being an edge connector, I don’t need one for each board (like “DuPont” or DIN 41612 does). If the board won’t be removed, you could even get away with the free tin plating (skipping gold).