I figured that would be the reasoning of your post. I don't disagree, though. The episode appeared to be more if a heavy handed slap at the idea of automated production more than about a lesson in particular.
"The old fashioned way works better ," however, doesn't hold up to scrutiny in this case. This was a single machine vs an entire family and it outperformed them and kept the quality up to snuff until Flim and Flam decided to bypass the quality control when more ponies came in to tip the speed in their favor. They still had a good way to make product. After the initial investment to produce more than a single machine, employing enough ponies to outperform the SSCS 6000 becomes cost prohibitive. In fact, having the Mane 6, Big Mac, and Apple Bloom ALL helping with the manufacturer, if not for the fact that they were volunteers or direct stake holders in the farm, comes to requiring eight full time employees working at maximum pace all day to match the output of a single SSCS 6000.
This episode comes off as both an infuriating backhand to industrialism, and rather badly argued.