I am pretty sure you know of older manuscripts that read different. And how far do the 9th century manuscripts go back to? Don't all manuscripts go back to the first century AD? That's a lot of manuscripts almost all with independent histories going back in time. The other reading died out. Doesn't seem like if it was original it would have died out?
No, they don't "all" go back to the first century. If they did then we could count them all the same and this would be easy.
Actually, the real question is why in the world "Son" came into existence in John 1:18 at all.
And we know why - because "begotten Son" is in John 3:16.
The question (as with 1 Tim 3:16) isn't "why did God die out if it was original" because that part is obvious - it seemed in contradiction to 3:16. But if "Son" is original, how in the world did "God" ever even come into existence so early?
It's an issue upon which there can be charitable disagreement in alignment with one's particular TC methodology; it isn't a hill worth dying on either way - unless, of course, you are a KJVOist who thinks EVERY hill is worth dying on (note: I understand you do not hold that viewpoint just to be clear).