Paul,
Yes all those things are true. The scetch is only going to work on the maple with that exact chip.
My original code would only run on the 2560, However it was reasonably well documented how to do it. I would expect that the same would be true of due. That in calling a timer one would have to know the pin map in relation to the timer and how the modification will affect the timer. I am also reasonably sure that it is possible to time up the due in a similar way. Basically the original code I used on the 2560 did the same thing prescaling the timer. Just did not have the ability to set the number of counts. That is provably also possible I just have not discovered it.
All is well, the maple is doing my bidding The due is communicating with the maple i2c or serial, much testing to do. Getting the due to run the interface the lcd touchscreen monitoring the battery, running the 12 v charging system many things for due to do. I am sure that as due matures pwm modification will mainstream in one form or an other. My pcb is ready for maple my first beta code for maple is meeting my expectation. My project is moving forward and soon I will drive down the road under ~duino control hopefully before Christmas.