I too had the belief that there was something special about the Arduino controllers, farther research has convinced me that isn't quite so. It appears they are pretty much std. stepper translator controllers and the Special Motherboard appears to serve as a buffer to the stepper controllers. At any rate, they make all the source code available free of charge, however; the website is a bit of a free for all as to how those files are organized. It appears Arduino source code will run across the Arduino platform by simply recompiling it. I am not too savy with C code as yet, but I read that somewhere. So if you are using something like Mach 3 with a 4th axis I think it will work.(the 4th axis controlling the extruder's stepper motor)
We're not in business to make parts, we're in business to make money, making parts is just how we do that.