The different colors serve to make the hills stand out. These are 'step type' wargame hills built to accommodate the rules. In this case, the rules stipulate that you end your movement at a linear barrier, and the base of the hills counts as one.
I actually like the layered look for these hills; it makes them looks like different strata from the surrounding red dirt plains. Sort of like the sandstone bluffs you see on Old Terra.
|Like this - only less dramatic.|