The cap is indeed inside of the socket. In this case though, it's a very tiny PTH cap (same as the blue ones used around the socket). The pads are large enough to mount an SMT cap in there if the socket is much shorter, or underneath if you don't use a socket.
But given the shape - I'm wondering why not swap the F USB for a M, give it a (removable) enclosure with holes/standard sockets in the side, and turn it into a key drive form factor? Keyduino?
Now the wheels are turning. I'm imagining the same design with a longer neck and a Male USB connector. Housed in an enclosure with 0.100 spaced screw terminals accessible through the sides and top. This would ofcourse require a CNC'd enclosure.
My only thought though is on usefulness; how useful is an arduino stuck directly to the USB port. On anything other than a laptop, it'd be stuck behind the machine somewhere and on a laptop it would need to be very tightly speced to make sure it didn't put too much stress on the USB port. The same enclosed design would work though with a regular USB-B connector and a short cable, allowing you to place the box on your desk.
Instead, I'm picturing more of a HardyDuino with a tough case, screw terminals, and some input protection. Much more suitable to deploying into harsher conditions, maybe with some outputs run on relays?