Yep, the option just tells the mobo chipset to be "aware" of SMART, and to keep an eye on it. The motherboard really has not much pull in updating the SMART tables.
HDD have firmware (OS) and run independent from the rest of the system. They perform their own maintenance all of the time.
The data that is stored on the HDD isn't even in the same pattern of binary as present on the OS. HDD use several types of encoding to work properly (RLL and PRML).
OS sees the hard drive as LBA (Logical Block Address), but the HDD internally still uses CHS scheme, and translates in real time between it's addressing, and the OS addressing.
It keeps track of SMART the same way, in real time without your knowledge.