Usually these pods are lifted by a crane and "inserted" in the building (talking of reinforced concrete buildings) after the structure has been built (before building the outer walls).

Once they are on the floor they are moved manually on carts/wheels attached to the pod structure, so it is much easier if everything is at the same level, the lowered level of the deck (only where the pod goes) would add another complication in the moving/placing.

With the advent of underfloor heating the thickness of the screed is increased anyway (compared to the old buildings) so the "step" is not anymore a problem as it was years ago.