The issue isn't that we have inverted wingers. The issue is that our inverted wingers are being supplied with the ball so deep because they're effectively wide midfielders who are on their wrong sides. Last night was a perfect opportunity to push the two wide men higher up the pitch and push Gross back in order to give more solidity to the midfield (as they were outnumbering us) and then allow our wide players to link more closely with Murray by running off him with pace in more of a 4-3-3.
But Hughton likes the system the way it is and I don't see that changing. I'd imagine that having two wide men on their stronger foots would lead to our full backs overlapping less and would lead to the middle two in midfield being exposed more, which is probably why Hughton does it.
You do see him telling them to change occasionally part way through games but you are correct he does seem to have a preference to play the inverted wingers. He did at Birmingham and Norwich as well but strangely, not when he was at Newcastle but that was probably because his main striker there was Andy Carroll and he probably preferred the wingers to cross the ball in that situation