I've heard many people swear by using the Brinsea spot check thermometer for checking accuracy, even those with hova's. If your using "separate temp/humidity reader" that is known for it's accuracy I'd say go by it, adjust. I don't know anything about hatching yet though so just my opinion. I think it is BS that you would pay so much for a incu to have to buy another more accurate therm to double check. I bought a Hova-Bator 1588 and will be firing it up in two weeks. I knew it was made of Styrofoam, WOW though, I'll have to be careful with it, hide it from the kids, they could tear it up in no time, super cheap almost dollar store quality IMHO, therm/hydrom better be accurate for that $$. Came with the IncuTurn turner, super cheesy also.
I'm fortunate at my job I have access to highly accurate state certified thermometers, and the Hova, when I checked...was dead on.
One miss-conception on calibrating thermometers is the ice bath method of 32 degrees...your only most accurate within the 32 degree mark, if you want to be accurate at 99-100 degrees you have to use a hot water bath method with a state certified thermometer. Know what they use? They're glass, with mercury in them....we can't buy those anymore though can we?