We consider an efficient scheme to simulate fermionic Hubbard models with nonlocal densitydensity interactions in two dimensions, based on bond-centered auxiliary-field quantum Monte Carlo. The simulations are shown to be sign-problem free within a finite, restricted parameter range. Using this approach, we first study the Hubbard model on the half-filled square lattice bilayer, including an interlayer repulsion term in addition to the local repulsion, and present the ground state phase diagram within the accessible parameter region. Starting from the antiferromagnetically ordered state in the absence of interlayer repulsion, the interlayer interactions are found to destabilize the antiferromagnetic order, leading to a band insulator state. Moreover, for sufficiently strong interlayer tunneling, we also observe the emergence of a direct dimer product state of mixed D-Mott and S-Mott character along the equal coupling line. We discuss the stability range of this state within strongcoupling perturbation theory. Furthermore, we consider the Hubbard model on the honeycomb lattice with next-nearest-neighbor interactions. Such an interaction is found to enhance both charge density and spin-current correlations within the semimetallic region. However, inside the accessible parameter region, they do not stabilize long-ranged charge density wave order nor a quantum spin Hall state, and the only insulating state that we observe exhibits long-range antiferromagnetism.