To clarify the situation
Using your definition, the Fourier transform is defined as following
\begin{align*}
\mathfrak F: \mathcal S(\mathbb R^n)&\longrightarrow \mathscr F(\mathbb R^n):=\{f:\mathbb R^n\longrightarrow \mathbb R\mid f\text{ is a function}\}\\
f&\longmapsto \hat f
\end{align*}
where \begin{eqnarray}\mathfrak F(f)(\xi)=\hat f(\xi)=\int_{-\infty }^\infty f(x)e^{2\pi ix\cdot \xi}\mathrm d x.\tag{1}\end{eqnarray}
You can also define
\begin{align*}
\mathcal F: L^1(\mathbb R^n)&\longrightarrow \mathscr F(\mathbb R^n)\\
f&\longmapsto \hat f
\end{align*}
but this definition is less interesting than the previous one since $\mathcal F$ will not be extendable to $L^2$ as easily (the only way to extend it to $L^2$ is to consider the restriction to function with compact support, but I'm not even sure if it's really enough). Anyway. Now, what you said (and your arguments are true) is that you can prolonge $\mathfrak F$ on $L^2(\mathbb R^n)$ using density of $\mathcal S(\mathbb R^n)$ in $L^2(\mathbb R^n)$ and completness of $L^2(\mathbb R^n)$.
This doesn't mean that for $f\in L^2$ unspecified it's Fourier transform is going to be given by $(1)$. It just mean that you can defined \begin{align*}
\tilde{\mathfrak F}:L^2(\mathbb R^n)&\longrightarrow \mathscr F(\mathbb R^n)\\
f&\longmapsto \tilde{\mathfrak F}(f):=\lim_{n\to \infty }\mathfrak F(f_n),\quad f_n\in\mathcal S(\mathbb R^n)
\end{align*}
such that $\left.\tilde{\mathfrak F}\right|_{\mathcal S(\mathbb R^n)}=\mathfrak F$. Notice that $$f=\lim_{n\to \infty }f_n,$$ in the $L^2-$sense. Then $\tilde{\mathfrak F}$ is called the prolongement of $\mathfrak F$ and is well defined by the argument you said.
Therefore, for $f\in L^2$ unspecified, if $f$ is in $\mathcal S(\mathbb R^n)$, then $\tilde{\mathfrak F}(f):=\hat f$ in the sense of $(1)$, and if $f\in L^2(\mathbb R^n)\backslash \mathcal S(\mathbb R^n)$, then $$\tilde{\mathfrak F}(f):=\lim_{n\to \infty }\hat f_n,$$
where $$\hat f_n(\xi)=\int_{|x|\leq n}f(x)e^{2\pi i x\cdot \xi}\mathrm d x$$ and the limit is of course taken in the $L^2-$sense.
Maybe you can notice that it's the same as $g:]0,1]\longrightarrow \mathbb R$ defined by $g(x)=\frac{\sin(x)}{x}$. You can prolonge $g$ on $0$ mean that there is $\hat g:[0,1]\longrightarrow \mathbb R$ s.t. $\hat g|_{]0,1]}=g$ and $\hat g(0)=\lim_{n\to \infty }g(x)$, but it doesn't mean that $g(0)=0$ (since $g$ is not defined at $0$).