Hi @Adeek, I have to leave shortly but I'll be back in an hour or so
but let me just say that I'm also slightly confused by what he wrote later about projectivising the equation. I don't think it's meant to be interpreted as "Here you have a bunch of equations in variables $x_i, y_j, z_k$ (say you have $n,m,l$ of them respectively), now consider your variety sitting in affine space $\mathbb{Q}^{n+m+l}$ and take its projective completion", because if you do this I don't think you necessarily have a map to $S$ basically for the same reason I said earlier about 1)