Passing USB signal over short SATA cable and connector
For a length of a few inches, twisted pair or not probably won't matter - ribbon cable will likely work just fine in most environments.

For option 2, I assume you mean something like this? (though probably with both ends female)


Those cables should work fine if you can find a source in the length you need - really short ones are probably uncommon though.  The fact that those cables aren't twisted for about an inch on each end is why I suspect you'd be fine without twisted pairs.

Those cables are for 2 USB ports, and are keyed so they can't be plugged in backwards - so you could use one set for your USB signal, and the other for the GPIO pins.