Here is a proof that if $X$ is smooth and proper over $\mathbb Z$ and of (relative) dimension $\leqslant 3$, then it is simply connected. The dimensional restriction is isolated to a particular step and I believe that theorem is conjectured to generalize to all dimensions.

Fontaine's letter to Messing proves that if $Y$ is smooth and proper over $\mathbb Z$, the Dolbeault cohomology $H^q(Y_{\mathbb Q};\Omega^p)$ vanishes off of the diagonal $p\ne q$ in low degree $p+q\leqslant 3$. I believe the low degree restriction is conjectured not to be necessary. By the Atiyah-Bott fixed-point formula, the Lefschetz number of an element of a finite group acting on a complex variety is the same as the Lefschetz number acting on its cohomology of the structure sheaf. Thus if $H^q(Y;\mathcal O)$ vanishes for $q>0$, Fontaine's theorem with $p=0$, then the Lefschetz number is $1$ and the action cannot be free. If $X$ were smooth and proper over $\mathbb Z$ with non-trivial pro-finite fundamental group*, then some finite cover $Y$ of $X$ would be canonical, thus defined over $\mathbb Z$ (eg, the composite of all covers of degree $\leqslant N$). Then $Y$ would be smooth and proper over $\mathbb Z$ with a free action by the finite covering group, a contradiction.

* If I recall correctly, there are varieties whose complex points have a nontrivial fundamental group, but that group has no finite quotients, and thus the étale fundamental group is trivial.