I finally found the time to type up an answer. The result is much less general than I first suspected, but I found it quite surprising that the regularity of the representation and the fact that it must be exceptional end up imposing such strong restrictions on the dimension vector of the representation. Maybe someone here will find it interesting, or, at least, mildly amusing too?
Let's denote the vertices of the $\tilde{D}_4$ quiver by $1,\ldots, 5$ with a single arrow $i\to 5$ for each $i\in \{1,2,3,4\}$. The indecomposable contravariant representations $V$ are then configurations of four subspaces $V_i$ in a vector space $V_5$. Let $S_i,\ P_i$ denote the standard simple and projective representations respectively. The Auslander-Reiten translate $\tau$ induces a linear operator on the Grothendieck group $K_0$, and its matrix $T$ in the basis $[S_i], i=1,\ldots,5$ satisfies
$$T=\begin{pmatrix}
0 & 1 & 1 & 1 & -1\\
1 & 0 & 1 & 1 & -1\\
1 & 1 & 0 & 1 & -1\\
1 & 1 & 1 & 0 & -1\\
1 & 1 & 1 & 1 & -1\\
\end{pmatrix},\ T^{2n}=\begin{pmatrix}
n+1 & n & n & n & -2n\\
n & n+1 & n & n & -2n\\
n & n & n+1 & n & -2n\\
n & n & n & n+1 & -2n\\
2n & 2n & 2n & 2n & -(4n-1)\\
\end{pmatrix}$$
Let $d_i=\dim V_i$ be the dimensions of the components of a regular representation, which are also the coordinates of its class in $K_0$. Then it is neither preinjective nor preprojective, so applying $T^k$ for any $k\in \mathbb{Z}$ should give us a nonnegative vector. In particular, we find
$$ \frac{\sum_{i=1}^4 d_i}{2+\frac{1}{2n}}\leqslant d_5\leqslant \frac{\sum_{i=1}^4 d_i}{2-\frac{1}{2n}}\quad \forall n>0,$$
so $2d_5=\sum_{i=1}^4 d_i$.
Now let's use the other condition. Note that the standard resolution of $V\neq P_5=S_5$ has the form
$$0\to P_5^{r}\to\bigoplus_{i=1}^4P_i^{d_i}\to V\to0,$$
where $r=\sum_{i=1}^4d_i-d_5$, and $r$ can be safely assumed to be non-negative, since $V$ is indecomposable, because otherwise we could find some number of $S_5$ subrepresentations. Let's look at what applying $\text{Hom}(-,V)$ does:
$$0\to \text{Hom}(V,V)\to \prod_{i=1}^4 \text{Hom}(P_i^{d_i},V)\to \text{Hom}(P_5,V)^{r}\to \text{Ext}^1(V,V)\to\cdots.$$
Since $V$ is exceptional, $\text{Hom}(V,V)=k,\ \text{Ext}^1(V,V)=0.$
Now we compute $$\dim \text{Hom}(P_j,V)=d_j,$$ so by counting the dimensions we have $$1+rd_5-\sum_{i=1}^4 d_i^2=0$$
Substituting $2d_5=\sum_{i=1}^4 d_i$ into this we can get an equivalent expression
$$
\sum_{\substack{1\leqslant i,j\leqslant 4 \\ i\neq j}}^n (d_i-d_j)^2=8.
$$
The solutions have the form $(d_1,\ldots,d_5)=(n+1,n+1,n,n,2n+1),\ n\in\mathbb{N},$ up to a permutation of the first four elements.
Let $N_{ij}$ be the indecompasable representation with $d_i=d_j=d_5=1, d_p=d_q=0$ for $\{i,j,p,q\}=\{1,2,3,4\},$ i.e. a configuration of two lines being identically mapped onto a single line. It can be manually checked that these 6 representations are exceptional and that $\tau(N_{ij})=N_{pq}$ in the previous notation.
It remains to show that all other regular representations with dimension vector of the form $(n+1,n+1,n,n,2n+1)$ (up to a permutation) can not be exceptional. Note that just by counting dimensions we find that such a representation $M$ must contain a subrepresentation $N_{12}\subset M.$ This means that $M$ and $N_{12}$ are in the same component of the Auslander-Reiten quiver. $\tau^2=\text{id}$ on this component, so by weaving the quiver we find that it consists of the representations $N_{12}=M_0,\tau(M_0)=N_{34}, M_i,\tau(M_i),\ i>0,$ with short exact sequences
$$0\to M_0\to M_i\to\tau(M_{i-1})\to 0$$
and irreducible morphisms $M_{i-1}\to M_i$ for $i>0$. Let's apply $\text{Hom}(M_i,-)$ to this sequence:
$$0\to\ldots\to\text{Ext}^1(M_i,M_i)\to\text{Ext}^1(M_i,\tau(M_{i-1}))\to 0.$$
If $M_i$ were exceptional, by the definition of the Auslander-Reiten translate we would have $$0=\text{Ext}^1(M_i,\tau(M_{i-1}))=\text{Ext}^1(M_i,\tau^{-1}(M_{i-1}))=\underline{\text{Hom}}(\tau^{-2}(M_{i-1}),M_{i})^*=\underline{\text{Hom}}(M_{i-1},M_{i})^*,$$
so we would have no arrows from $M_{i-1}$ to $M_i$ in the AR quiver, which is impossible. This argument basically shows that if an exceptional regular representation belongs to a component of the AR quiver on which $\tau^2=\text{id},$ then it must belong to its 'border'.
All in all, we have shown that the only exceptional regular representation of $\tilde{D}_4$ are the 6 representations $N_{ij}.$