Well, i haven't used it exactly like this in exactly this application, but yes, i have used an AD like this. This is one of the reasons why there is the possibility to use external Vrefs.
It's always a good practice to use the same source for both Vrefs for exactly the reason you mentioned. However, in this application that's not really necessary since the voltage you're measuring is not dependant on your reference. This means that you need a very stable(ripple free) and accurate(known voltage) reference. Vdd is most likley not good enough. There are about a gazillion different ways of creating this Vref, easiest is to buy a chip from Maxim. Trimming of your potentialdividers is also(probably) necessary to get the precision you're after. If it's a "one off" i'd do that with potentiometers, if it's going to be made in big quantities i'd do the trimming in software.

To finish this off, i'd like to say that you're shooting WAY over the target for a batterycharger. Millivolts is not important in this case, tenths of a volt would be enough.

But that's just my humble opinion .......

Good luck,
/Ingvar