Thanks for your contribution. I don't necessarily disagree with your position, but the documentation (even the complete data sheet) isn't entirely clear on what / how these registers are programmed. Further, there is a serious shortage of programming examples in Atmel's documentation for these chips (well, in our opinion anyway).
All references to the Sam3A4C registers include stuff like setting timers as peripherals, using nested interrupts, programming the timers and cascades; all without examples and/or any guiding principles.
Consequently it is difficult (if not near-on impossible) for those of us without experience with this chip to even begin to explore its potential. Even using the Arduino IDE - which is still in Beta stage - we are still experiencing issues - it's early days yet.
For now, we are getting a relatively clean 9Khz signal over which we have full control - because it is software generated. We can modify the waveform - if and as we please. We can change its duty cycle - even by fractions of a percent if needed, and - because the waveform is generated in software - we are able to synchronise it accurately across multiple Arduino Due's.
So, in conclusion, yes - all things being equal your point is entirely valid.
However, until there is more clarity for us on how to accurately program the registers, and until we are able to identify some examples out there that we can piggy-back on, this does the job for us.
It's not an ideal world out there; we simply get the job done for now.
J.