What I'd like to know is whether there is any substance to his statement that the spine is in a stronger/safer anatomical position when bent over as opposed to upright.
I don't think so, no. And I get most people to squat that way, just not for most of the reasons he says. Of low, high and front squats, the low is the most difficult to perform and coach properly. This is one thing that makes it good for newbies, mastering a difficult challenge on day one helps them want to come back. Other aspect is, most people come in all hunched over, doing the low-bar properly stretches out the tight pecs/shoulders, and makes them tighten up the weak upper back. So it's good for newbies. What's good for people already strong might be something else, but as I always remind people:
Starting Strength. Most people forget that, including SS coaches and Rip.
I don't think anything is as important as consistency, just keep showing up and lifting. Lots of people make a big deal out of these sorts of differences, playing their gurus off each-other.
Rippetoe says, "low-bar back squat."
4 million WL coaches say, "high-bar back squat."
Dan John says, "barbell front squat."
Pavel Tstatsouline says, "goblet squat."
You could argue about their differences, but what do they have in common? You have to squat. So to my mind, that is where the real truth is.
I had a guy come to me wanting to learn the low-bar, he'd been doing high-bar. I said, "You already squat 140kg for work sets, forget it, keep doing what you're doing." He insisted, we tried it, it hurt his shoulder, old injury there. "Keep doing high-bar," I said.
"But -"
"No, seriously."
I get most newbies to low-bar, but I don't think it's a big deal, and if you're doing something else and it's working, why fuck with it. Really, just squat.