  The creation of moir\'e superlattices in twisted bilayers of two-dimensional
crystals has been utilised to engineer quantum material properties in graphene
and transition metal dichalcogenide (TMD) semiconductors. Here, we examine the
structural relaxation and electronic properties in small-angle twisted bilayers
of metallic NbSe$_2$. Reconstruction appears to be particularly strong for
misalignment angles $\theta_P$ < 2.9$^o$ and $\theta_{AP}$ < 1.2$^o$ for
parallel (P) and antiparallel (AP) orientation of monolayers' unit cells,
respectively. Multiscale modelling reveals the formation of domains and domain
walls with distinct stacking, for which density functional theory (DFT)
calculations are used to map the shape of the bilayer Fermi surface and the
relative phase of the CDW order in adjacent layers. We find a significant
modulation of interlayer coupling across the moir\'e superstructure and the
existence of preferred interlayer orientations of the CDW phase, necessitating
the nucleation of CDW discommensurations at superlattice domain walls.
