Does anyone know if installing an aftermarket running board will void the factory warranty?
No more than using non-Mercedes brand fuel.
The only thing that can void a warranty is something that specifically causes a failure that would otherwise be covered by the warranty. And even then only that is stricken from the warranty, everything else is still covered.
Only thing I can quickly come up with for running boards is whether the installation exposed something which later rusts.
As for me, I sat in a W166 with and without running boards and had a definite preference for without. But when an otherwise near perfect W164 appeared with running boards, I bought anyway. I would consider taking them off but its too much trouble due to the high level of integration into the car.
I find it harder to step on the running boards to get out than to step over. And I find it harder to step over the running board than to step over when there wasn't a running board.
My previous F-250 4WD was tall enough that running boards were not an option. Am 6'-1" and the only way in was to grab the handle on the A pillar and step up on the running board.