The UNO has 1.1v internal voltage reference for ADC, and the ARM-based Maple has a 1.2v interval voltage for ADC (ADC1, channel 17). Reading the SAM3X8E reference manual, I don't think the DUE has an internal voltage reference for ADC. Is this true?
The DUE's ADC does have a gain that can be configured to trade precision for range.
Yes that is right it only has a pin Vref input.
Have you read the application note on the A/D, document number 11106A
That tells you all about it.