Pascal
1. I think that you need to be careful with "resolution" and "accuracy". The ADC has 16 bit resolution but maybe not 16 bit accuracy. I believe that about 14.2 bits of accuracy is achievable when the sampling and HW averaging is optimised. Lower accuracy will be obtained when sampling is not optimised and less accuracy again if the circuitry is not well constructed to keep out noise for the power supply, references and signals.
2. Usually the ADC reference value doesn't affect resolution - Ain == VREF should always give full scale - 0xffff in 16 bit mode - the quantisation levels are simply smaller when the reference voltage is lower. But accuracy may be affected since any fixed level noise will be proportionally higher when the reference voltage is made lower.
Regards
Mark