Not a cosmologist, so I'll defer to any simulators who are more up-to-date with the field than I am, but the papers linked from wikipedia are about the fitting of models to existing data, and by using a more complete model, they can better constrain values in the models; whereas the massive 3D simulations are looking at a different problem, and go through a rigorous level of validation and cross-checking, with different microphysics tested and examined. Both dark matter and dark energy fall out of GR—they can both be zero, but they can also be non-zero.