Where does the motherboard temp reading come from?

it comes from a small themo diode some where on the motherboard. each motherboard puts it somewhere slightly different so its hard to tell you where it is unless you list your specific motherboard. in general it is considered your temp of the air inside your case as a thermostat measures your temp for your house(note some rooms are colder or warmer just as inside your computer some areas are cooler and warmer but its a close average). safe temp is a mater of opinion and system design. I personally would say anything under 40c is ok but not ideal under 30c is best. again it will depend on who you ask.