I claim that every autohomeomorphism of $M$ is conjugate to an extension of an autohomeomorphism of the Cantor space.
Let $B$ be the Stone space of the Cantor space. Let $\overline{B}$ denote its Boolean completion. We shall show that every automorphism of $\overline{B}$ is conjugate to an automorphism of $B$. Recall that $\overline{B}$ is up-to-isomorphism the only complete atomless Boolean algebra with a countable basis (by a basis, I mean a subset $A\subseteq\overline{B}$ where $\overline{B}=\{\bigvee R:R\subseteq A\}$; for example, $B$ is a countable basis for $\overline{B}$). Suppose that $h:\overline{B}\rightarrow \overline{B}$ is an automorphism. Then let $D\subseteq \overline{B}$ be the smallest Boolean subalgebra closed under the operations $h,h^{-1}$ and which contains the countable basis $A$. Then $h$ restricts to an automorphism $g:D\rightarrow D$, and $h$ is the unique automorphism of $\overline{B}$ that extends $g$. Recall that every countable atomless Boolean algebra is isomorphic (the theory of countable atomless Boolean algebras is $\omega$-categorical), so $B$ and $D$ are isomorphic. Let $\phi:B\rightarrow D$ be an isomorphism. Then $\phi$ extends to an automorphism $\Phi:\overline{B}\rightarrow\overline{B}$. In this case, $\Phi^{-1}h\Phi:\overline{B}\rightarrow\overline{B}$ is an automorphism that uniquely extends an automorphism of $B$.
One can extend this argument to conclude that if $(h_n)_{n=0}^\infty$ is a collection of automorphisms of $\overline{B}$, then there is some
automorphism $\Phi:\overline{B}\rightarrow\overline{B}$ where for each $j$, the mapping $\Phi^{-1}h_j\Phi$ uniquely extends an automorphism of $B$.