I can appreciate the dude was going for humor. But the premise dead ends at what is convenient.
I didn't really see it as an attempt at humor. I saw it more as a way for us to get a more "real" sense of and appreciation for how good we have it, and where things really come from. I've heard that many kids these days (and some adults, too!) don't realize that food comes from crops/farms or animals. They think it is literally created the way they find it packaged in the grocery store.
Just a few years ago someone wrote a hatemail to a hunting TV show saying something to the effect of "Shame on you for killing animals! If you want meat, go buy it at the store so an animal doesn't have to die!"
That said, I also agree with you that in order to follow his logic of "I'm making everything from scratch myself" I found myself saying "You didn't make that boat. You didn't make that knife. You didn't make that oven. You didn't make those seeds. You didn't make that [whatever]" etc.
Jimmy John's is actually pretty good. I'd take them over Subway any day, and I used to really like Subway. Depending on your opinion of Subway, that may not be saying a whole lot. YMMV.
I had Jimmy Johns once. It was OK. I still prefer Subway.