Several things to mention here Dan.
It is wrong to call infrared energy light energy. It is an electromagnetic wave, just as radar or sound are. The wavelength of the typical IR bands, 3-5 um and in the case we're talking, 8-12 um, are much higher than light. Your eye only "sees" to the high .7 um, low .8 um.
The higher the temperature, the less difference the coating makes. This is one of the reasons why a cavity blackbody is an optimum calibration source. (That and the elimination of reflections.)
Areas of discoloration aren't very important on a part under test - to some degree. One of the reasons I use VHT flameproof paint, is that it bakes into the metal somewhere around 300 C. It might look like crap, but it does perform well. When you paint a part, it's ok to slightly see the metal underneath. If you have too much coating, it may be insulating the part.
If you were going to perform a lower temp test, the best paint is Krylon ultra flat black. This is a high carbon paint and very emissive, E= 0.95 Trouble is, it doesn't stick to well either and flakes off at higher temperatures.
I agree that you can't get good results with Raytecs, or any other devices of that nature. The only instance I know of that they are used with some degree of accuracy is race car tires. But then, I don't think the E of the rubber varies much either.