You could fill it less, but personally I would just run with it as is... I have no issues hatching guinea eggs in my incubator using a 2oz bottle as reference, they generally hatch on day 26 though, but I don't believe that is a higher temp issue as many other members have said their guinea eggs also hatch in about the same 26 days, not the 28 advertised...
I purchased a veterinary grade glass analog thermometer and used the at verify the calibration of my digital probes... But if you go this route you have to pay attention to the type of vet thermometer you get, you DON'T want a 'knock down' one, these have a little zig-zag pattern on the mercury/alcohol channel at the bottom and they are designed to read and hold the max temp achieved... These 'knock down' ones were the kind that were very common for taking body temps back in the day, when you would see a doctor shake the mercury back down with a few flicks of the wrist before taking the temp...
Or you can take some distilled water and boil it and confirm it reads your altitudes boiling temp keep it at a low boil when measuring, then take some more distilled water and fill a glass half full then fill it the rest of the way with ice (preferably ice made with distilled water) stir well and give it a bit so the ice starts to melt and verify it reads 32°F or 0°C I prefer to keep stirring while taking the readings... Distilled water is preferred for the most accurate readings but not absolutely necessary... Some may question why you use an ice/water mixture to measure freezing, it's because the measurement is the point where water freezes and ice melts, ice alone can actually be much colder...
Google your locations altitude then reference this chart for boiling points http://www.engineeringtoolbox.com/boiling-points-water-altitude-d_1344.html
Don't skip the above, a few hundred feet of altitude changes the boiling temp and could toss off your calculations... Also calibrate all your thermometers at the same time in the same boiling and freezing water, while giving them a few minutes to get accurate readings...
There is no right answer beyond the fact that you most certainly want it open once the chicks start to hatch to provide them with fresh air... If you can maintain temp and humidity with it open all the time go that way, if not you might need to plug it every so often...
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