I do agree that the Sam... datasheet register are not very detailed, maybe a mix of Atmel releasing too early beta datasheet or whatever.
You might want see this video where I'm using the four 16-bits MEGA timers, each being specifically delayed 90°, 180°, 270° with less than 62.5 ns
P.S. In fact, there really SIX 16-bit timers, two of them are being emulated by my specific protoshield using some 74HCxy chips
Just hoping the arduino team will soon fix the USB serial issue via a new IDE release, at least on my side I cannot afford to migrate my actual project MEGA software using very advanced timer register tricks since i'm shuttling more than 5000 VAR's with my igbt's drivers, blue smoking and $$$ gone !
Once DUE serial USB will be OK, I'll look deeper on the DUE timers which i feel from datasheet are very very interesting with fascinating new features.