IMFD's manual discusses the mathematical methods used, and it can use a couple. Range-Kutta (sp?) is default, I believe. Most IMFD programs use a two-body solution, but IMFD's Map considers more than just the vessel and reference planet. If you hit <MOD> (in IMFD Map) until you get to Map's configuration page, it will tell you how many bodies it is currently including in it's calculations.
AFAIK, TransX uses conical sections.
Neither is "real", but are somewhat realistic future tech. These MFD's have access to information about the vessel's exact position, etc, that aren't currently available without ground observers and sattelites that don't yet exist.
In real life, spaceflight is done by pre-planning every burn well before launch, using high order math that isn't possible in a realtime simulation such as Orbiter. Then the plan is tested in a simulator (not a realtime sim), and the simulation can easily take longer than the actual flight.
It's entirely possible, that in the future when spaceflight becomes much more common, that navigation tools similar to IMFD may be created - but that's going to be quite a while.
