The Cornfield TV-B-Gone uses one battery for the microcontroller and the other for the IR LED.
The Vf of an IR LED is much lower than a visible LED, so the current is quite a bit higher (if not limited by a resistor). If only one battery was used, then the voltage would drop below what the microcontroller needs to operate. So two batteries are used to allow maximum IR LED current and reliable operation of the microcontoller. Remotes that use a single battery limit the IR LED current with a resistor so the battery voltage does not drop too much.
Lithium coin cells should not be connected in parallel. The weaker battery will discharge the stronger battery and life will be greatly reduced.TV-B-Gone Generation 1,2,3 Schematic