I doubt if commercial scenery payload is directly connected with this, it is just trying to pack high amounts of detail into a small area. But I must say with modern computers I don't think much in FS2004 bothers it.
The sad thing is that all of the data for roads, rivers and railways is cheaply available from SatNav developers, so they could be easily corrected today but we are playing with twenty year-old software of course. It has been done for FSX, so that they then blend perfectly with accurate mesh, but unfortunately FS2004 roads, rivers etc are generated differently and are not backwardly compatible with those in FSX.
Trying to change the world manually, like ViperPilot2 has is a challenge too large for me! I choose to turn a blind eye to things like that.
John