I agree, but this is a problem at the scenegraph level - Coin3D uses single-precision floating point and since the next option (OpenSceneGraph) is the same, there's no way to really fix it.
The solution, if it can be accomplished, lies in data segmentation, I think. And I think how the data gets divided up really depends on the type of modeling that's being done. I could be wrong about that, though.
In any case, before a general solution can be proposed for FreeCAD, it needs to be prototyped. And really, I think this problem is really limited to the sort of datasets that you and I work with - geospatial stuff. So if a solution is to be implemented, it should be done here.
In any case, I'm willing to at least kick it around a bit and see if I can make something work - but I need your dataset to do that - and maybe an example post, showing exactly where the errors appear.