The end points as to how the join a corresponding piece of both systems is totally different. I would think if you cut that portion out of the way by removing the end ties. It would be just a matter of shimming the MTH higher and using the Atlas rail joiners to join the outside rails to keep them in line. You may need to shim under the MTH rail to get the joiner to fit snug and keep the rails at the proper height. Then again. When you consider a lift bridge. Nothing is in place at either end and yet the rails still line up close enough. I know HO guys use different coded track as far as rail height and transition the 2 to go from mainline trackage to a yard area. You can slip a tie or 2 in place under the rails with basswood and spike them if needed. As far as the center rail. I think you could file a notch in the railhead and solder a rod in place or just leave a gap and create an isolated block.
All this is speculation asI have never done it other than Gargraves to Atlas which involved trimming the underside of the Gargraves rail to accept the Atlas joiner. I’d just experiment with some pieces and see if it’s doable. I think if it was only a matter of a few spots that needed the transition I’d give it a shot.