First of all this is an absolutely superlative answer it almost brought me to tears: https://math.stackexchange.com/a/3791368/758507
I am fairly certain that all compact 3 dimensional Nil manifolds (manifolds admitting Nil geometry) are nilmanifolds (admit a transitive action by a nilpotent Lie group). Every compact 3d nilmanifold (besides the torus which is abelian) is of the form $N_r:=H(3, \mathbb{R})/\Gamma_r$ where
$$H(3, \mathbb{R}) = \left\{\begin{bmatrix} 1 & x & z\\ 0 & 1 & y\\ 0 & 0 & 1\end{bmatrix} : x, y, z \in \mathbb{R}\right\}$$
is the three dimensional Heisenberg group, and
$$\Gamma_r = \left\{\begin{bmatrix} 1 & a & \frac{c}{r}\\ 0 & 1 & b\\ 0 & 0 & 1\end{bmatrix} : a, b, c \in \mathbb{Z}\right\}$$
where $ r $ is a nonzero integer. For a reference see theorem 5.4 bottom of page 25 in https://arxiv.org/abs/0903.2926 . I just want to confirm that these nilmanifolds $ N_r$ exhaust all compact 3d Nil manifolds. In particular I believe $ N_r $ is just the mapping torus of $ T^2 $ associated to $$ \begin{bmatrix} 1 & r \\ 0 & 1 \end{bmatrix} \in SL_2(\mathbb{Z}) $$ where again $ r $ is a nonzero integer. At this point it is worth mentioning that $ N_{\pm r} $ are diffeomorphic and moreover the mapping tori associated to the four matrices $$ \begin{bmatrix} 1 & \pm r \\ 0 & 1 \end{bmatrix}, \begin{bmatrix} 1 & 0 \\ \pm r & 1 \end{bmatrix} $$ are all diffeomorphic.
If the $ N_r $ are all the compact Nil manifolds then by guess is correct. If there are other compact Nil manifolds then my guess is wrong. Again my question is:
Is every compact Nil manifold a nilmanifold?