We must assume that if it is matter, Genesis can work with it.
...But solely for the purpose of turning it into life-generating matter, according to Marcus. You can't build a planet (or a star!) out of moss.
Yes they do certainly rise.
Not on camera, I don't think. The camera simply moves along the surface, marred with craters visible from great heights. About thirty seconds into the ride, we close in on fuzzy orange mountains which then turn grey and sharp and then acquire snowcaps as the landscape acquires water and vegetation. The zoom-in would obscure all evidence of cratering: the mountains we see would not have been visible in the early moments of the simulation at all. In the subsequent zoom-out, water in turn obscures everything.
To say that mountains "rise" in the transition from fuzzy orange to sharp grey is overstating the case: there is no vertical movement there to be seen.
I'd say the orange fuzziness is the exact same thing we see on the main viewer after our heroes have made good their escape. It just lingers longer in reality than in the simulation. And involves just the sort of small scale changes demonstrated in the simulation.