Let us denote by $F$ the extension of the Fourier transform to $L^2(\mathbb{R}^n)$ as described in the OP, and denote by $G$ the analogous extension of the inverse Fourier transform to $L^2(\mathbb{R}^n)$. We know that $FG=I$ and $GF=I$ on the Schwarz functions; the question is if it is true on $L^2(\mathbb{R}^n)$. The answer is yes, and the answer below is in a more general topological space setting, because this abstraction illustrates the underlying phenomenon more clearly. Apart from continuity, the main reason why it is true is the density of the Schwarz functions in $L^2$ and the Hausdorff property of $L^2$ (because its topology is induced by a norm).
Claim. Let $X$ and $Y$ be topological spaces, where $Y$ is also Hausdorff. Let $A,B:X\to Y$ be continuous maps, satisfying $Ax=Bx$ for all $x\in S$ for some dense subset $S\subset X$. Then $A=B$.
Proof. Pick $x\in X\setminus S$, and let $a=A(x)$ and $b=B(x)$. Consider arbitrary neighbourhoods $V$ and $W$ of $a$ and $b$, respectively. Then by continuity, there is an open neighbourhood $U$ of $x$ such that $A(U)\subset V$ and $B(U)\subset W$. By density, there is $s\in U\cap S$, hence $V\ni A(s)=B(s)\in W$, meaning that $V\cap W\neq\varnothing$. Since $V$ and $W$ were arbitrary, and $Y$ is Hausdorff, we conclude that $a=b$.