PGA is programmable Gain Amplifier.
Could I set internal voltage ref and yet leave the resistor on the side it is currently? Since I am only looking at the difference between the two voltages?
No, as it shown on your circuits there is about 5V at voltage divider outputs, and ref. voltage can't be lower than that.
BTW, what part number of ATTINY you gonna to use? Look in data sheet, if it supports differential mode and PGA. Something to think, otherway 10 OHm resistors may be an answer.