The game cartridge provides no suitable connection that would allow the Retrode to directly sense the presence of the battery, measure its voltage, etc.
The battery is supposed to power only the save RAM, not the other ICs of the cartridge. Also, it must not be "charged" by the regular supply voltage from the NES/... (there is at least one diode in the cartridge to prevent this). I therefore believe that the battery is "isolated" so that its voltage cannot be measured through the cartridge connector, not even at the cartridge's power supply pins.
The Retrode can only look at the data in the game's RAM and make a guess if that's meaningful game data (battery backed) or just what that particular RAM chip likes to initialize with.