This shows a fundamental lack of how SMS works. Which is fine, I'm not trying to criticize!
SMS (whether inside the drive or on the logic board) works by retracting the read/write head to the parked position whenever the laptop experiences sudden motion or free fall. This makes it so the head cannot come into contact with the platter (where all the data are stored). When it's internal to the HDD, the whole process is handled by the HDD itself.
It can't be "system-wide" unless the logic board is programmed to look for a HDD in every possible place, which it isn't. It's only programmed to look in the HDD bay. It IS built into the logic board, but it still only applies to the HDD bay.
Also, that clicking noise you're referring to: it isn't the HDD rattling around inside the computer, it's the read/write head inside the HDD clicking and not being able to move properly, spelling death for the HDD. Just because you can't hear that clicking doesn't mean that the on-board SMS is working, it just means your HDD isn't broken.
Solution: make sure your HDD has its own SMS and leave it in the optical bay.
Yeah, that's referring to the SMS on the logic board. It seems that person is unaware that HDDs can also self-contain a SMS and that the SMS has no effect on speed unless you are trying to use your computer while in free-fall (apart from malfunctions on the part of the SMS).