fat16lib has been posting quite a bit about ADC noise and the "low noise" mode in the Storage section recently.
I suggest you have a read. Bottom line is it appears the low noise mode does not make an appreciable difference. Also if you're getting the sort of noise you suggest it's likely on your end , not the atmel.
fat16lib did some fairly rigorous testing and found noise <=1LSB.
I also have and external cct with 8 op-amp buffers feeding into a Uno and I don't even see movement in the last digit.
That's all rather good news because the ADC sleep mode takes out MPU for extended periods so it's a heavy performance hit. Also there's more you can do to fix your external circuit than you can do about the noise on the atmel ADC.
This is one aspect of the hardware I'm quite impressed with.