First of all, that video you just posted pretty much shows they're made with machinery, they are factory made. Humans are made completely different and the fact that you're comparing the 2 is fairly laughable.
Synths may need to eat, drink, and breath, sure, but they don't age. Synths are stuck at the same age permanentely, rendering the fact that they're just like us completely irrelevant. If a person stays the same age their entire life and never shows any sign of aging/growing up, that makes them vampires or one of the Lost Boys, not a normal functioning person. This, also, makes the so-called child synth even more disturbing when you realize Shaun wants you to look after a 10 year old boy forever, like in that cruddy movie AI by Stephen Spielberg.
Only some parts of them are biological. They still run off machinery to function. That skeleton and outer coating on them isn't human, it's what makes them tick. Before they get the skin and organs/muscles slapped on them they basically look like a stripped down Gen 1 Synth.
I would chalk up there not being a synth component on every Gen 3 Synth being more about game balancing than part of the lore. It's stated in-game that Synths run off this Component. In fact, if you sneak behind a Gen 3 Synth and steal their component, it kills them instantly. Thus if every single Gen 3 Synth + Courser had these they'd be way too easy to kill, thus it's a balance issue, not proven lore.
And for that matter, you're wrong about Covenant. They're slowly learning how to distinguish the two. Dr. Roslyn Chambers (this lady:
http://fallout.wikia.com/wiki/Roslyn_Chambers ) states that the SAFE test now has a 1 in 4 chance of finding a Synth, and for that matter, she was completely right about that girl she has trapped down there. If you let Chambers fry that girl whom she claims is a synth, you can go up to that girl's body and see that she is, in fact, a Synth. So clearly there are some differences in the way a Synth's "brain" is hardwired compared to a human's.