[guided]The difficult case is when the two points share neither coordinate. Let
\begin{align*}
P=(x_1,y_1), \qquad Q=(x_2,y_2),
\end{align*}
with $x_1 \neq x_2$ and $y_1 \neq y_2$. The vertical and horizontal lines through $P$ cannot contain $Q$, so if a line through both points exists, it must be one of the symbol lines through $P$.
For each $i \in I$, the symbol line through $P$ coming from $L_i$ is
\begin{align*}
S_{i,L_i(P)}=\{(x,y)\in X\times X:L_i(x,y)=L_i(P)\}.
\end{align*}
Together with the vertical and horizontal lines through $P$, define
\begin{align*}
\mathcal{M}_P := \{V_{x_1},H_{y_1}\} \cup \{S_{i,L_i(P)} : i \in I\}.
\end{align*}
There are $2+(n-1)=n+1$ lines in this collection.
We now check that these lines overlap only at $P$. The line $V_{x_1}$ and the line $H_{y_1}$ meet at exactly $(x_1,y_1)=P$. A symbol line $S_{i,L_i(P)}$ meets $V_{x_1}$ only at $P$ because, in the row $x_1$, the symbol $L_i(P)$ appears exactly once, namely at the column $y_1$. Similarly, $S_{i,L_i(P)}$ meets $H_{y_1}$ only at $P$ because, in the column $y_1$, the symbol $L_i(P)$ appears exactly once, namely at the row $x_1$.
Finally, take two distinct indices $i,j \in I$. The point $P$ lies in both $S_{i,L_i(P)}$ and $S_{j,L_j(P)}$. Orthogonality says that the ordered pair of symbols
\begin{align*}
(L_i(P),L_j(P))
\end{align*}
occurs at exactly one cell of $X \times X$. Since it occurs at $P$, it occurs nowhere else. Hence
\begin{align*}
S_{i,L_i(P)} \cap S_{j,L_j(P)}=\{P\}.
\end{align*}
Each line in $\mathcal{M}_P$ has $n$ points. Since all $n+1$ lines share the point $P$ and otherwise are pairwise disjoint, their union contains $P$ plus $n-1$ additional points from each of the $n+1$ lines. Thus
\begin{align*}
\left|\bigcup_{M \in \mathcal{M}_P} M\right|
=
1+(n+1)(n-1)
=
n^2.
\end{align*}
But $\mathcal{P}=X\times X$ also has $n^2$ points. Therefore these $n+1$ lines through $P$ cover all points of $\mathcal{P}$.
Since $Q$ does not lie on $V_{x_1}$ or $H_{y_1}$, it must lie on at least one symbol line $S_{i,L_i(P)}$. It lies on at most one such symbol line because two different symbol lines through $P$ meet only at $P$, and $Q \neq P$. Hence there is a unique $i \in I$ such that
\begin{align*}
Q \in S_{i,L_i(P)}.
\end{align*}
This is exactly the statement that
\begin{align*}
L_i(x_1,y_1)=L_i(x_2,y_2),
\end{align*}
and the unique line through $P$ and $Q$ is $S_{i,L_i(P)}$.[/guided]