Actually in this case the MCP3913(Like the MCP3911 which I use) can measure +/- .6V referenced to AGND. Max input is +/- 2V, but signals outside of the +/- .6V range won't be very accurate. They do caution about holding inputs below AGND for any length of time, or if the internal clock is not running.
As far as the voltage reference goes, what kind reference are you using that has better specs(9ppm/C tempco) than the internal? Beating the internal VREF is hard because at that level everything counts, how long your traces are, how clean the board is, solder type, etc. These are not like some MCU vrefs that might have a 500ppm/C tempco or worse, where adding even a $2.00 external reference makes a big difference.