Thanks to the comments for pointing out the rookie error. This is fixable by using the density of continuous functions, but probably overcomplicated.
Let's first argue this for continuous $f$, for which we can use the following generalisation of the DCT (see this for a proof): let $h_n, g_n, h, g$ be integrable functions such that $h_n \to h, g_n \to g$ a.e., $|h_n| \le g_n,$ and $\int g_n \to \int g$. Then $\int h_n \to \int h$.
Let us work with the extended definition of $f$ you mention. Let $\{x_n\}$ be any sequence converging to $0$, and define $g_n = f(x_n+t)^2 + f(t)^2$. Then due to continuity of $f$, $g_n \to 2f(t)^2$, and since integrals over $\mathbb{R}$ are invariant to translation, $$ \int_{\mathbb{R}} g_n = 2\int f(t)^2 = \int g.$$ But $|f(x_n + t) f(t)| \le g_n,$ we conclude that $$ \int_{[0,1]} f(x_n+t)f(t) = \int_{\mathbb{R}} f(x_n + t) f(t) \to \int_{\mathbb{R}} f(t)^2,$$ where the equality uses that $f(t)$ is $0$ for $t \not\in [0,1]$. Since $\{x_n\}$ was arbitrary, it follows that $F$ is continuous at $0$ (although nothing really used $x_n \to 0$ in the above, so the argument works for continuity at any $x$).
Now to move to $f \in L^2,$ we can use the density of continuous functions in this space. Concretely, let $M = \|f\|_2,$ and fix $\varepsilon \in (0,1)$ and take $\varphi$ to be a continuous map such that $\|f-\varphi\|_2 \le \varepsilon.$ Then for every $n$, \begin{align} &\qquad \left| \int f(x_n +t) f(t) -\int \varphi(x_n+t)\varphi(t)\right| \\&\le \int |f(x_n+t)(f(t) - \varphi(t))| + \int |\varphi(t) (f(x_n+t) - \varphi(x_n + t)| \\ &\le 2\|f\|_2 \|f-\varphi\|_2 = 2M\varepsilon. \end{align}
It follows that $$ \limsup \int f(x_n + t) f(t) \le \limsup \int \varphi(x_n+t) \varphi(t) + 2M\varepsilon = \int \varphi^2(t) + 2M\varepsilon.$$
But $\|\varphi\|^2_2 \le \|\varphi - f\|_2^2 + \|f\|_2^2 + 2\|f\|_2 \|\varphi - f\|_2 \le \|f\|_2^2 + (2M + 1)\varepsilon$ telling us that $$ \limsup \int f(x_n+t) f(t) \le \int f(t)^2 + (4M + 1)\varepsilon.$$
Similarly, we have the lower bound $$ \liminf \int f(x_n+t) f(t) \ge \int \varphi^2 - 2M\varepsilon,$$ and $$ \|\varphi\|^2 \ge \|f\|^2 - 2\|f-\varphi \|\|\varphi\| - \|\varphi - f\|^2,$$ giving us that $$\liminf \int f(x_n +t) f(t) \ge \int f(t)^2 - (4M + 1)\varepsilon. $$
Now, since $\varepsilon$ is arbitrary, drive this to $0$ to conclude.