actually I think I read that it would be better for your transmission to have it tuned? But none the less having the ATX tuned will be a great improvement.
For what it costs for a tune I would do some more mods (intake, exhaust, etc) and then get a complete engine tune that includes the ATX (shift points, trans pressure, etc), make it worth your while.
If your serious about getting the tune talk to Tom or FSwerks.
2010 Ford Escape 3.0 V6
2004 F350 6.8L V10
1986 XR4Ti 2.3L Turbo
2007 ST ; formally bewst'd - R.I.P