It is not straightforward to do in GROMACS what CHARMM can do rather easily on a script-based level, hence why you do not get this option when generating inputs from CHARMM-GUI. To keep water out of the bilayer, you would need to implement flat-bottom restraints, which requires both topology and coordinate file manipulation. Equilibrate without it, and if you get any water leaking into the membrane, there are other ways to deal with it, but I would avoid trying to directly replicate the CHARMM approach.