I am not sure about the mounts but I would bet the cam, compression ration and few other things with the motor itself would be different. I believe the R1 revs to like 13500rpm or there abouts.
The pistons and rod are the same but the head , block and crank are different. The rx1 and apex were purpose built engines that were derived from the r1 but built for a snowmobile.
redline is 13750rpm ti valves fly by wire fi forged alum pistons the r1 is pretty tricked in stock form make over 180hp.the new 2012 apex picked up a few of the r1s new stuff, like longer intake tracks & exup valve tech tha apex makes over 160hp now.
Modeled after the R1 of the late 90's. The current R1 and current Apex motors are different animals all together. Intake, electrical, heads, and cams etc are all over and beyond what Yamaha will dress the Apex up in.