Understanding and controlling the orbital alignment of molecules placed between electrodes is essential in the design of practically-applicable molecular and nanoscale electronic devices. The orbital alignment is highly determined by the molecule-electrode interface. Dependence of orbital alignment on the molecular anchor group for single molecular junctions has been intensively studied; however, when scaling-up single molecules to large parallel molecular arrays (like self-assembled monolayers (SAMs)), two challenges need to be addressed: 1. Most desired anchor groups do not form high quality SAMs. 2. It is much harder to tune the frontier molecular orbitals via a gate voltage in SAM junctions than in single molecular junctions. In this work, we studied the effect of the molecule-electrode interface in SAMs with a micro-pore device, using a recently developed tetrapodal anchor to overcome challenge 1, and the combination of a single layered graphene top electrode with an ionic liquid gate to solve challenge 2. The zero-bias orbital alignment of different molecules was signalled by a shift in conductance minimum vs. gate voltage for molecules with different anchoring groups. Molecules with the same backbone, but a different molecule-electrode interface, were shown experimentally to have conductances that differ by a factor of 5 near zero bias. Theoretical calculations using density functional theory support the trends observed in the experimental data. This work sheds light on how to control electron transport within the HOMO-LUMO energy gap in molecular junctions and will be applicable in scaling up molecular electronic systems for future device applications.