Maybe you're right regarding the formation, it could be a way to put a fresher Young on the left, while allowing Valencia on the right to have less ground to cover.
On the other hand, it's a pity we're leaving both Mata and Martial on the bench, although I'm not sure the fact they're more rested and been training with the team won't give them a big chance to start instead of Mkhitaryan and Lingard, respectively.
They could easily start, especially in that 3-4-3 formation where the two behind the striker don't have to track back that much.
There could be several reasons for José's change to this formation. One is probably the lack of a proper defensive midfielder in the team. Carrick in a way is, but doesn't play that much. I think Mourinho prefers Pogba-Herrera duo, but has tried it and noticed there's a big weakness in lack of discipline and cover for the back four. Another could be the LB situation. As we have no-one near Valencia's level on that side, this way we have more support for whoever plays there.