Edit: It turns out that the system you're dealing with is very different from the systems I'm familiar with. Hence more or less everything below is wrong, with regard to that system. I'd simply delete the whole thing but I can't since it's "accepted"...
The reason your version makes no sense is it's false. You're leaving out a crucial hypothesis; what's true, and what it had better say in the book, is this:
If $\Sigma\vdash\phi$, where $x$ does not occur free in $\Sigma$, then $\Sigma\vdash\forall x\phi$.
That makes much more sense. Informally, saying $x$ does not occur free in $\Sigma$ means that the formulas in $\Sigma$ do not say anything about $x$. So saying $\Sigma\vdash \phi$ where $x$ does not occur free in $\Sigma$ means "you can prove $\phi$ without assuming anything about $x$".
Now it makes sense. If you can prove $\phi$ from a set of assumptions that don't mention $x$, then $\phi$ follows from your assumptions regardless of what $x$ is, so $\forall x\phi$ "should" also follow from the same assumptions.
Taking $\phi$ to be $x=1$ is a bad example, because it's hard to imagine a system where you can prove $x=1$ without assuming anything about $x$. Instead imagine you have some axioms describing how the real numbers work, and you want to prove $\forall x(x>1\to x^2>1)$. If you can prove $x>1\to x^2>1$ without assuming anything special about $x$ then $\forall x(x>1\to x^2>1)$ follows. (That is how people prove $\forall x\phi$ in actual math: prove $\phi$ without assuming anything about $x$.)
Hmm. An example of a $\Sigma$ where $\Sigma\vdash x=1$ but $x$ is not free in $\Sigma$ would be $\Sigma=\{\forall y (y=1)\}$. Yes, $\forall y (y=1)$ implies $x=1$, and it also implies $\forall x (x=1)$.
Another example, illustrating how if $x$ does occur free in $\Sigma$ then all bets are off: It's true that $x=1\vdash x=1$. But $x=1\not\vdash \forall x(x=1)$. If you leave out that "where $x$ does not occur free in $\Sigma$" then you're going to conclude that in fact $x=1\vdash\forall x(x=1)$, which is nonsense; luckily $x=1\vdash\forall x(x=1)$ does not follow from the correct version of the result we're talking about.