@Cy I have been looking around to see if anything meets all of the criteria that you are looking for. One of the closest is the new Salsa Timberjack XT 29. The drivetrain is mostly XT and it is 12 speed. The brake are Shimano but not the XT line.
Cannondale has a Trail 2 29er but the only part on it that is XT is the rear derailleur. But that model only has 11 speeds. Both are great bikes. Good luck in your search!
Perhaps someone else will chime in with a bike that more closely matches what you are looking for.