The concedpt of using temperature to determine metabolism and thyroid status was developed by Dr. Broda Barnes some time ago. He got patients to put a thermometer in the armpit for 5 minutes before getting out of bed in the morning, had coffee, food or done anything significantly physical. He preferred an axillary temperature rather than the mouth because "so many people have low grade unsuspected sinus infections that generate heat only in the oral cavity thereby falsely raising the oral temperature."
So it was just a way of trying to assure the most accurate temperature result possible. If there is no sinus infection, then oral temperatures are fine, but they have to be compared to a different reference range.