First off, "entire evolution of the universe" should obviously be qualified with "on cosmological scales", unless they've built the matrix. That said, how big is the domain? Is it just set to match the observable universe? 2048 grid points across the entire universe (or just the observable universe) seems rather... low-res. The TFA mentions an adaptive grid, but fails to mention what factor that can increase the local resolution by.
As you point out, the 'entire evolution
Also, how exactly do we model dark matter when we don't really know WTF it is beyond the fact that it has gravitational mass? Does it work because gravitational effects are the only thing that really matters on cosmological scales?
Essentially, yes; gravity absolutely dominates at these scales compared to all other forces considered. The role of stellar and galactic feedback into their environment when forming (and as they evolve) changes lots of important things, but simulations like Bolshoi seek to simulate the largest scale structures in the universe. Smaller subsections of the simulation can be picked out to run detailed N-body simulations of Milky Way type galaxies, or to statically match the dark matter clumps (which will form galaxies) to huge databases like the Sloan Digital Sky Survey. Both of those are pretty active things-to-do in cosmology now.