There are some constructions we can do from here that seem consistent with this intuition. We can define the one-edge and one-vertex graphs: \[ \mathsf{edgeGrph} : \mathsf{Grph} \qquad \mathsf{edgeGrph}\ \E\ \partial = \E\] \[ \mathsf{vertGrph} : \mathsf{Grph} \qquad \mathsf{vertGrph}\ \E\ \partial = 1\] Let's say the "graph homomorphisms" $G_1 \imp G_2$ between two graphs $G_1\ G_2 : \mathsf{Grph}$ are the maps that work uniformly for all $\E$, $\partial$, i.e. maps in \[ (\E : \rset) (\partial : 2 → \E) → G_1\ \E\ \partial \to G_2\ \E\ \partial\] Then we can say the vertices of $G$ are the homomorphisms from $\mathsf{vertGrph}$ to $G$ and the edges of $G$ are the homomorphisms from $\mathsf{edgeGrph}$ to $G$.
By using parametricity we should be able to see that a graph homomorphism \[[V_1, E_1, d_1] \imp [V_2, E_2, d_2]\] is actually the same thing as a pair of maps $V_1 \to V_2$ and $E_1 \to E_2 + V_2$ that are compatible with $d_1$ and $d_2$. (The $+ V_2$ is present because it is allowed to map an edge in $E_1$ into the reflexivity edge of a vertex) By the pushout UMP, the main things we need to confirm are that \[(\mathsf{vertGrph} \imp [V_2, E_2, d_2]) = V_2 \tag{*}\] \[(\mathsf{edgeGrph} \imp [V_2, E_2, d_2]) = E_2 + V_2\tag{**}\] In the $\mathsf{vertGrph}$ case, the only terms of the pushout that we can build given $(\E : \rset) (\partial : 2 \to \E)$ are either $\binr v$ for some $v \in V_2$, or else $\binl \langle \partial t, e\rangle$ for $t : 2$ and $e : E_2$. But the latter is equal to $\binr (d_2 e)$ by the imposed pushout equality. So the only real possibilities are $\binr v$, and we see the isomorphism $(*)$ holds.
In the $\mathsf{edgeGrph}$ case, we have one additional variable in the context, and we're trying to build a term of the pushout given $(\E : \rset) (\partial : 2 \to \E) (\varepsilon : \E)$. We can make $\binr v$ for $v : V_2$ as before, or else $\binl \langle \partial t, e\rangle$ for $t : 2$ and $e : E_2$ as before, which doesn't add any new real terms, but now we can do $\binl \langle \varepsilon, e\rangle$ for any $e : E_2$. So the isomorphism $(**)$ holds.
But unlike that presheaf category, whose objects are exactly the reflexive graphs, there's a lot more junk lying around in $\mathsf{Grph}$! For consider the "graph" \[g_{???} : \mathsf{Grph} \qquad g_{???} = \lambda \E \partial . (\E \to \E)\] Now consider the maps from this into the edge graph: \[g_{???} \imp \mathsf{edgeGraph} = (\E : \rset) (\partial : 2 \to \E) \to (\E \to \E) \to \E\] This is the church encoding of a type that is two copies of the natural numbers.
So this weird exotic graph object knows how to "fit into" each vertex in countably many different ways?