IIRC the SAM can do PWM using either the timers or the dedicated PWM engine. Arduino (presumably to keep compatibility with previous boards) use the timers.
It's the PWM engine that has the H and L versions of the PWM signals but they aren't used by Arudino, which is not to say some of the pins aren't broken out to headers, if so you can learn how to drive the PWM engine and use them.
DUE-Pins 4/87 and 10/77 (PA29/PC26 and PA28/PC29). Why are those Pins crossconnected to each other?
You'll have to ask the Arduino designers about that, we've talked about it before and AFAIK nobody can figure out why that was done, especially as it stuffs up the external memory interface.
As for reading the temp sensor, you'll have to read more and get down and dirty with the registers (I think).