I'd agree. Re-extrude the door so it's flush with the hull, while leaving the gap. This can in turn be used to bake a normal map.
I will state that I'm not a fan of the over-accentuated upper docking mount. I'd personally rather see the smooth(er) original shape of the Hermes retained while the details are enhanced. Furthermore, be careful not to stray too far from the design with engine details - though the Hermes was always blocky, it did maintain the appearance that it could be shot out of something. If you break up the surface too much, you'll lose that design characteristic.