Since the original article mentioned redundancy and planning for failure, I think we have to factor in the cost of parts when discussing launch costs. After all, it's the cost to launch a replacement. (Notice my $50k figure included the cost of parts for our backup flight unit plus the launch costs.)
I think you're right that automated factories in space will reduce the actual launch costs (just the cost of getting your junk into space). The rest of the cost reduction has to come from reducing the cost of manufacturing. Accepting additional risk can certainly help here. That's a big change of mindset for the aerospace industry.
In my example, the cost of materials and manufacturing was a fraction of the actual launch cost. I don't think that's typically the case for traditional spacecraft, but I'm not positive about that. Adding more or heavier parts increases the mass, which requires more energy from the launch vehicle to reach orbit. I find it entirely plausible that adding redundancy increases launch costs as well as manufacturing costs, but I don't know how the big boys arrange their launch costs. (At PolySat, our satellites were so small that we paid per kilogram. Other satellites can be the size of a van or even a school bus.)
I think 20 years is a bit optimistic for space-based factories to reach the point where we can dramatically lower the costs of launching a spacecraft. I think a kilogram of aluminum mined in space and a kilogram of aluminum mined on Earth would not be fungible, and would thus have very different costs. Initially, I think the aluminum available at the space-based factory would cost significantly more than ground-based aluminum. (The company that builds the factories will have to recoup their costs, as will the companies that mine the raw materials. And at least initially, they're going to be paying to launch those spacecraft from Earth.) Eventually, we could reach a scale that the cost of materials in space is low enough to seriously discount traditional launch costs. I just think there's a lot more than 20 years of work to get there.