I tried few times to rotate an freeze transform after, result is strange, model looks ok on the preview but in game like in the last shot. Or do you propose to rotate only bones?Hmm, I'd go with the Y-up, centimeter version, but make some changes in maya. First unbind your mesh from your rig then rotate "bone_root" 90 degrees on the x axis in maya, then remove all history and bind your model to the skeleton again.
Sadly but I could not get the result I neededYes only the bones.