To my understanding, it's a way to get a highly accurate measurement of the frequency response of your microphone. Once that is used, any deviations the microphone has from a perfectly flat frequency response can be added or subtracted from any room, speaker, etc. measurements you make.
Without a calibrated microphone, some peaks or dips in any room, speaker, etc. measurement you get may be a result of the peaks or dips in the microphone's response. In simple terms, a calibrated microphone will tell you (or room measurement software) where to "fix" the measurements of your room, etc. by taking into account these peaks or dips in the microphone itself.
This may not be a perfect answer to what you're looking for, but it's what I understand it to mean. So, someone please correct me if I'm wrong
Paul