Update:
I spoke with an Apex support engineer today. He described the FMM auto detect feature in a bit more detail and explained why they recommend using auto detect: If an optical sensor fails but it's not set for auto detect, the readings from the faulty sensor could cause harm to the tank and you wouldn't know the sensor is faulty. If auto detect is on, the sensor would be disabled and not report faulty data.
Now that the update seems to be running stable on my FMM modules, I'm going to give auto detect another chance to see how it works for me. If it does work as advertised, that would be another layer of protection I didn't have when manually setting sensor types.