Oh yeah they will definitely be a LOT different if they are in different locations. On my egg the temperature can be close, or one can be 15 degrees hotter. Which probe is hotter depends on how it feels that hour, as they can swap which one is hotter during a cook. To get the AC filter you need the linkmeter snapshot too (you're missing the configuration option if you just do the AVR snapshot).
The noise graph on the home page, you're looking to see what the range of the error is and if it is consistent. It should theoretically be a straight line or have at most 2 numbers it is going back and forth between. If it is all over the place drifting about you have a problem. If it is a sine wave then with a period equal to your AC mains frequency, it's a AC problem.
As far as "calibration", HeaterMeter can't really be calibrated because you're only doing a 1 point calibration. Thermistors are non-linear so calibrating will only get you accurate temperatures at the calibration point. The thermocouple is a little better but it should be 5.000V +/-2.5%.