Microsoft has a launch parity clause (developers can only release their titles on Xbox One if they haven't already been released on other consoles). There's an article I found on IGN about it: http://www.ign.com/articles/2014/04/01/microsoft-discusses-xbox-one-launch-parity-clause
That's not the direct reason though. There's nothing to prevent SuperGiant from releasing Transistor on Xbox One day and date with PS4 in theory. I'm guessing there is some kind of exclusivity deal in place with Sony and SuperGiant likely wouldn't have resources to do three versions at the same time anyway. If Microsoft waives launch parity (which they have in the past and likely will do more frequently in the future) then we could see Transistor on Xbox One.