As I said, I could be wrong, but I had thought the dealer told me there was a different part # for the fender flares with the running boards (which would mean a total of 4 different part #'s for each corner of the car if you also take into consideration the 20" wheel models already use a special flare). The running boards have a few pros and cons as I see it:
Pros: Looks better (especially with the 20" wheel option)
Useful for small kids to climb in or out without stepping on the carpet and door seals (if you can train them to use them).

Cons: Adds cost (although marginal if bought as a factory option)
The staining issue makes people worry about keeping them looking good
For normal sized adults and teens they get in the way and can soil your pants when you rub against them when entering/exiting
The ground clearance issue (although I am not sure if this is actually true, and for many it would make no differnence in the suburbs!)

The rocker panel cover is the large black plastic trim piece that connects the front and rear fender flares together.