Both sensors both use a MEMs-based microphone and are very similar in their response to sound.
The major benefit of the Microphone, order code MCA-BTA, $44, is the flexibility of the "wand" style form factor for positioning the sensor in an experiment.
The MCA-BTA also tends to perform better at longer distances from the source of sound. The internal microphone can only measure sounds very close to the face of the LabQuest.
The internal sensor tends to register larger difference (maximum to minimum) in sound pressure for a given tone. However, it can tend to drift up in value over the course of a standard 0.03 second experiment.