you're missing that most computers come off the shelf with Windows and all the other crapware pre-installed. Reinstalling windows is something you and I can do in our sleep... but many users can't.
No, I'm not missing that. I'm just saying that most of us don't need to engage in the careful art of real "system tuning".
IMHO, if Best Buy were charging people $40 to reinstall the OS and drivers from scratch, install all of the applications the customer wanted (and none that they didn't want), and do some basic post-install configuration (set up user accounts, click "OK" on all the EULAs, install all updates, etc.), then I would think that wasn't a bad value. In fact, if that was a service that they would do for any computer you brought in, assuming they did a good job at it, then I might advise computer novices to take their computer in for that service every year or two.
I'm guessing that's not exactly what they're doing, though.