Just going back to the question of sockets/pins. the extended headers yes with a bit of effort you can remove the lower part, this you can then add to the pins under the board, giving you another 2mm of spacing to the the USB and power sockets...
That's the trick. They are not the ones with which most of us are familiar, and which are used on the standard Arduinos or commonly sold for use with them. They are obviously taller, so if they were
used on an Arduino board - one available with the headers separate - you would obviously not have this complaint in the first place.
I usually put a piece of electrical tape on top of the USB socket when I use shields.
Maybe, maybe not. To my mind "electrical" PVC tape is too soft, and too easily penetrated by projecting wires particularly if there is movement. As long as there are no such wires - no components/ through-hole wires or jumpers, it should be OK, but I would prefer a more rigid material such as acrylic or of course - polycarbonate sheet.