This will be a partial answer, leaving one case unresolved. The answer is obtained by applying the results of the Culler--Vogtmann paper linked in your post. That paper focusses on the $F\mathbb R$ property of a group $G$, which says that every action of $G$ on an $\mathbb R$-tree is trivial (meaning that there is a point fixed by the whole group); this applies to actions on simplicial trees, which are a special class of $\mathbb R$-trees.
Let $M_{g,r}$ denote the mapping class group of an oriented surface of genus $g$ with $r$ punctures.
In Section 3 of the Culler Vogtmann paper you'll find an extensive list of examples of groups to which their main theorem applies, showing that each of these groups satisfies property $F\mathbb R$. Flipping to page 682 of the Culler Vogtmann paper, you'll see that this list includes:
- $M_{g,r}$ for $g \ge 2$ and $r \ge 0$
- $M_{0,r}$ for $r \ne 4$, $r \ge 0$ (for some reason that paper switches to the notation $M^r_0$ instead of $M_{0,r}$).
That settles those cases.
Regarding the three mapping class groups $M_{0,4}$ and $M_{1,0}$ and $M_{1,1}$, each has a homomorphism onto $\text{PSL}(2,\mathbb Z)$ with very small kernel. The group $\text{PSL}(2,\mathbb Z) \approx \mathbb Z / 2 \mathbb Z * \mathbb Z / 3 \mathbb Z$ has its standard Bass-Serre tree action on the 3-valent tree. It's not hard to prove that this is, essentially, the only tree action of $\mathbb Z / 2 \mathbb Z * \mathbb Z / 3 \mathbb Z$, and with a bit more thought regarding the behavior of kernels, this should settle your question for these three mapping class groups, because if a group $G$ has a finite normal subgroup $N$ then $N$ is contained in the kernel of any action of $G$ on a tree.
To be a bit more specific: $M_{1,0}$ and $M_{1,1}$ are both isomorphic to $\text{SL}(2,\mathbb Z)$ and hence both have a homomorphism onto $\text{PSL}(2,\mathbb Z)$ with kernel cyclic of order $2$. Also, $M_{0,4}$ has a split homomorphism onto $\text{PSL}(2,\mathbb Z)$ with kernel isomorphic to $\mathbb Z/2\mathbb Z \oplus \mathbb Z / 2 \mathbb Z$.
So, what's left are the groups $M_{1,r}$ for $r \ge 2$. Each of these groups has a homomorphism onto $M_{1,0} \approx \text{PSL}(2,\mathbb Z)$, by "filling in the punctures", and thus we get an action on the trivalent tree by composing this homomorphism with the standard action of $\text{PSL}(2,\mathbb Z)$.
So, your question about transitive actions remains unresolved in the case of $M_{1,r}$ for $g \ge 2$.
If I may sharpen your question just a bit, we get the following:
- Does every minimal action of $M_{1,r}$ ($r \ge 2$) on an $\mathbb R$- tree factor through the standard Bass-Serre tree action of $M_{1,0} \approx \text{SL}(2,\mathbb Z)$, via the canonical "puncture forgetting" epimorphism $M_{1,r} \mapsto M_{1,0} \approx \text{SL}(2,\mathbb Z)$ (up to automorphisms of $\text{SL}(2,\mathbb Z))$?