[...] The control register has a 24 bit key - do you know if it works as a seed?
That key is actually just for write-protecting the register. Many of the SAM3X8E's built-in peripherals require a security key (to protect against run-away code overwriting the registers?). With the Timer Counters, for example, one of the peripheral's registers is the Write Protect Mode Register. You need to write the security key to that register before you can write to most of the other registers in that peripheral.
The True Random Number Generator has so few registers that, rather than having a separate one for controlling the write-protection, they combined the security key and the bit for enabling the TRNG in the Control Register. For the TRNG, the key is always 0x524E47 (which is "RNG" if viewed as ASCII characters). So, to enable the TRNG you write 0x524E4701 to that register, and to disable it, you write 0x524E4700.
Hope that helps!