I suspect it's more about who operates the machine and whether they know how to properly set it up, etc.
With those big box stores, there's often too much turn-around in staff that by the time they're using the machine properly they end up in a different dept or leave for a better job, etc.
It's no different than the oil change service at your local dealer or fast-lube place ... it's always the rookies doing those jobs and I've seen and heard of the stories there.
Having said that, yea you may get some old-timer who's been working the key cutting machine for years at the local Cdn Tire and he's the go-to guy to get paged when you show up.
With a locksmith, you've got a professional doing the job all the time.