I too was quite frustrated at TransX while trying to figure it out. I couldn't understand the manual so I learned TransX by trial and error. It took years before learning enough to realize that, as written, TransX was not able to do something like planning a trip from the moon to planets other than Earth (both using and not using the Earth's gravity well). But it was after learning what was possible that it became creatively obvious that a ghost or surrogate ship allowed a way to plan when otherwise no plan was possible. Maybe not using a manual encouraged a more creative use of TransX?
Should TransX be used in a way not specifically designed for? I believe that being creative to modify intended uses to accomplish what otherwise isn't possible is a worthy goal. Yesterday a tractor I intended to operate suddenly had a faulty ignition switch. The key would go to "on", but the "start" (starter motor) contact failed. I took 2 screw drivers and excited the starter solenoid from the 12v input of the starter, and started the tractor. I'm not worried that the designer of the screw drivers never intended the tools to be used for this particular purpose. If I didn't have screw drivers I would have used a belt buckle and a quarter or whatever else I could get my hands on to do the job. Mechanical work is filled with the creative use of tools. Niel and Buzz would agree, reference using a pen to toggle a broken switch.
And as far as whether using a ghost ship is an attack on realism? Heck, even the "T" button to warp time is an attack on realism. But we all know it's an absolute necessity.
Realism is what you pretend it to be. For example, you could pretend to be sitting on the moon, with a "real space ship". And in this space ship you pretend to have a real computer with a copy of Orbiter and TransX booted up for flight planning. In this onboard computer you can pretend to create an imaginary ship in orbit around the Earth that you can use to both set up a flight to Mars as well as for you to target with your "real ship". After the planning is done you then pretend to launch your "real space ship" from the moon for your Earth gravity well burn trip to Mars. Ultimately, if you are able to manually fly from the surface to the surface of another rocky sphere you can pretend that you made a "real flight" and everything else such a ghost ships, were just onboard tools to enable the flight.