Because graphene is atomically flat, if you apply an overall gate to the whole structure all you do is move the potential landscape by a constant amount, but the energy zero level is anyway arbitrary so nothing changes in reality.
On the other hand, you are a bit mistaken about "the Fermi level in graphene" because
a) you have no gate where there is a Fermi level defined (in the electrodes), and
b) where the gate is applied there will be an effect locally, and this will show up in the transmission spectrum. But in the middle of the device the electrons are not in equilibrium so there is no Fermi level.