I think the point is that for filaments to form in simulations you have to assume dark matter to be so abundant that it stops explaining other things that are explained with it. Basically you can adjust dark matter parameters to explain everything but you can't find a single set of parameter values to explain all the things at the same time.
That's not the case. The hydrodynamical simulations mentioned use the same cosmological value set by CMB data. The ratio is not the same in every galaxy, because matter and DM behave differently on small scales, but this variation comes out naturally in simulations.