Orbiter uses the planet diameter to place your launch pad and spacecraft at zero level on the surface.
On Earth, the diameter is sea level, so Orulex terrain is always above sea level and the base looks like a crater if located in an elevated area. Also, there's a parameter to control if the "crater" has a rim or not. If not, it's just a hole in the ground with a specified diameter.
For the Moon or Mars, Orulex can draw bellow the average planet diameter. In that case, bases can become an elevated mountain.
This would only be solved if Orbiter itself supported an elevation parameter for each base.