The field of quantum simulations in ultra-cold atomic gases has been remarkably successful. In principle it allows for an exact treatment of a variety of highly relevant lattice models and their emergent phases of matter. But so far there is a lack in the theoretical literature concerning the systematic study of the effects of the trap potential as well as the finite size of the systems, as numerical studies of such non periodic, correlated fermionic lattices models are numerically demanding beyond one dimension. We use the recently introduced real-space truncated unity functional renormalization group to study these boundary and trap effects with a focus on their impact on the superconducting phase of the 2D Hubbard model. We find that in the experiments not only lower temperatures need to be reached compared to current capabilities, but also system size and trap potential shape play a crucial role to simulate emergent phases of matter.