Subfloor Thinner than the Underlayment
What matters is the total thickness of the floor to support your finish floor. Tile manufacturers require certain thicknesses going under their products as well as some makers of "decouplers" that isolate the movement of wood under a tile floor. Laticrete and Schluter come to mind here. If it is vinyl flooring the surface needs to be smooth. The thickness of either layer does not matter which level it occupies. My preference would be to set the same thickness in the same level as original. Only thing I may do different would be to use a better grade material than the original if possible. Plywood not OSB, not particleboard. The more layers in the makeup of the plywood the better.