Indeed, just last night I saw a short video about the Starship launch pad. Along the way someone quoted someone at SpaceX saying they didn't know how to build Starship yet. So yes, that casts the whole process of constructing flight-test articles in more favorable light. You can dig up photos of early assemblies from the lunar module and space shuttle showing them being assembled with hand tools on plywood fixtures. It's a matter of understanding where we are in the process.
Without delving into a lengthier response...
Generally you have to develop the thing you're building and the way you're going to build it together. Fabrication and assembly methods place constraints on the design, and it's costly to ignore them until later. So I'm just not sure where the Starship is in its development process. If the contention is that one company outpaces all others, then you need to take careful stock of what they might be skipping and why. My impression is that Elon Musk prefers a Silicon Valley style engineering development process, which is hardly surprising. You work very quickly to build prototypes and proofs of concept, then you go back later and fill in the gaps, redesigning as necessary to accommodate things you learned during your initial work. This seems to work well for software and electronics, although those of you who specialize in those fields can correct me.
But the manufacturability issues don't resolve themselves easily that way when the product is a costly physical engineering article. The Falcon 9 acceptance was delayed because NASA inspectors kept finding nonconforrmant manufacturing and assembly processes. The Tesla Model 3 was delayed for the same manufacturability reasons. I drove a demonstration model and was impressed enough with it to plunk down the deposit for one. A year went by, and then another year. The price kept going up and the feature list kept getting shorter. This was Tesla trying to figure out how to build it after it had already been "designed." And lest this turn into a one-sided criticism, it's also the reason the Dreamliner was late. Boeing tried to cut the same corners and paid the price in a costly redesign effort and delayed delivery.
That said, if you can afford to learn from failure then it's worth it to explore other development processes and see if you can find a better way. So just because you aren't doing the same thing everyone else does doesn't mean you're doing it wrong. It just means it falls somewhere else on the cost-benefit spectrum. Now in the case of Falcon 9 you can clearly say that the manufacturing issues are resolved, because the delivery tempo is enviable. But the question is how big a check Elon Musk had to write to fix the manufacturing variances? And what if it had happened in a company where that sort of correction wasn't an option?
More importantly, manufacturability is not strictly an economic argument. If you're going to do work for a national space agency, acceptance testing based on a manufactured product is the requirement. And it's the same for some commercial customers (or more appropriately, their insurers). A one-off, hand-built article isn't eligible for acceptance testing because a lot of the other requirements of a development and manufacturing process (which I'll get into in a separate post) have to be baked into the process. The tests aren't just for the article, but for the way the article is being designed and built. You have to demonstrate that you can make an article that passes various tests using a process that also satisfies certain criteria that pertain to the process. You have to prove you can do it that way every time, not just for the article submitted for test.
So the answer to why Starship prototypes are currently being assembled with general purpose construction equipment is simply that it's not as far along in the development process as I had previously thought, and SpaceX have elected to accelerate to flight testing. And from what I understand the objectives of these test flights to be, I have far less a problem with the construction methods now that the evidence seems to show not only that they're building up the actual production line, but that they're doing it fairly early in the process. This is good, because it means they seem to be addressing a problem that has plagued Musk's companies before.
