In chiral magnets, magnetic skyrmions are typically stabilized by the competition between exchange and Dzyaloshinskii-Moriya (DM) interactions under an external magnetic field, while the role of lattice degrees of freedom has received comparatively less attention. Here we study how spin-phonon (SP) coupling modifies magnetic interactions and the resulting spin textures in a two-dimensional skyrmion model in the square lattice. Using Monte Carlo simulations, we compare two simplified models describing the SP coupling: the Einstein site-phonon (ESP) and bond-phonon (BP) models. Integrating the lattice degrees of freedom, we obtain effective Hamiltonians for each SP model, which involve three-spin interactions and quadratic terms. In both cases, skyrmion crystals are stabilized in field regimes that are topologically trivial in the uncoupled model. Moreover, in certain regimes, the conventional triple-$\qv$ hexagonal skyrmion lattice is distorted into a double-$\qv$ square skyrmion lattice. Additionally, we find that, in the ESP model, strong phonon coupling affecting the exchange interactions drives the system from typical low-field helical phases to meron-antimeron crystals with no net chirality. Overall, our results show that lattice effects provide a simple mechanism to tune a wide variety of topological magnetic phases, ranging from typical skyrmion crystals to distorted arrangements of skyrmions, elongated bimerons and meron-antimeron phases.