Actually, there is a difference between the RTR and the Genesis motors. But I think as far as the space inside the locomotive is concerned, they are basically interchangeable. Especially if your RTR motor uses the newer hex-drive shafts.
Moreover, you could swap it out with a Kato motor with flywheels. The Athearn hex drives just happen to fit the hex holes in the Kato motor flywheels. I’ve done this on a couple of older Athearn BB locos and have been very happy with the results. And the bonus was I didn’t even have to break out the Dremel to cut up the frame! You could order directly from Kato. If you do, they sell one version of the motor with what they call an “older style” integrated plastic mount that is a drop-in fit for an Athearn RTR chassis (see it here). Another source is Ulrich Models, which sells the motor w/o the plastic mount, but you can get the A-Line motor cradle weight to mount the motor on. Their website has instructions on how to do this.
Note: I’m not an employee, spouse of an employee, shareholder or otherwise affiliated with Kato or Ulrich Models… or A-Line… or Athearn… (did I miss any? [:P] )… Just a satisfied customer passing along my own personal experiences! [:D]