In any event, the effects in the Himalayas are quite dramatic: Everest is about 9km high, but the Moho boundary is pressed 30km deeper below the Himalayas than below the surrounding land; and similarly under the Andes.
You can't expect perfect equilibrium--for the weight of rock above to equal the weight of rock pushed down. Spalling and erosion will remove a lot of the excess above, and on a timescale much faster than continental drift. Still, that's a lot of rock "under water".
Of course there may be some biases in their reconstruction; they can't measure the depth directly, and there could be some error in the correction terms they use to account for the continental rock.
Something else to keep an eye on.