I've seen a few programs that can do CSG very well indeed, but most of them are not speed-critical, Lightwave, Vue D'Esprit etc all have powerfull boolean setups, but the problems arise, from what little I can remember, when trying to do this with optimised graphics data, I seem to recall that FS2's lack of geomodding is to do, in part, with the way the models are stored, but this was mentioned several years ago, so I can't remember the details.
Vue in particular is good, because it's a real-time CSG, similar, I think, to 3DS Max, if you create a boolean with two objects, the system doesn't just subtract one from the other (or whatever the operation is) and store the results, it actually keeps the two objects that are interacting, and you can alter the boolean effect by moving/resizing the objects involved. The negative side of this is that it only works with basic shapes, i.e. Spheres, Cubes etc, whereas Lightwave can boolean anything with anything else as long as there are no points that are in precisely the same place in both sides of the operation (and with the usual problem associated with CSG operations, like problems with complex objects).