We study scaling limits of periodically weighted skew plane partitions with semilocal interactions and general boundary conditions. The semilocal interactions correspond to the Macdonald symmetric functions which are $(q,t)$-deformations of the Schur symmetric functions. We show that the height functions converge to a deterministic limit shape and that the global fluctuations are given by the $2$-dimensional Gaussian free field as $q,t\to 1$ and the mesh size goes to $0$. Specializing to the noninteracting case, this verifies the Kenyon-Okounkov conjecture for the case of the $r^{\mathrm{volume}}$ measure under general boundary conditions. Our approach uses difference operators on Macdonald processes.