My main point would be if you start him in the middle (as an a/m not as a second striker where his back is to goal) then all of a sudden he's got 3 potential passes on being rooney through the middle, Depay running from the left and then the right winger i.e. Januzaj who would be running in on his stronger foot. Not to mention if he's already central he can make the pass quicker. We've got wide players in Depay/Januzaj who would naturally be wanting to make a run inside and we've got Mata who's by far our best player at spotting those runs. Multiple runners would open up the pitch as teams wouldn't be able to just flood the middle.
When Herrera plays and Mata is wide it's not such an issue as they've clearly got a good understanding and Herrera uses the ball a lot quicker than Depay/Januzaj do centrally which helps Mata, but as a natural fit Mata as the third midfielder with two wingers making inside runs seems like a good idea to me. There will be some games where maybe the other team presses too quick and Mata can't find space where he might be better of wide but I can't see the hard in trying that set up, although right now I'd be happy going with a front 4 of rooney, mata, depay and herrera.