Ah, for that you should probably look at Maurice's StepUp tools. In general you can either concentrate on making a pretty visual model (VRML export) or a Solid Model for use in various applications (creating an enclosure, FEM, etc) but you can't really mix both. For KiCad I only care about the mechanical model and not the visual model so I dont even make an attempt to provide both. I think Maurice's tools provide the best way to manage both the visual and mechanical models.
I had a look at the code regarding that message; I think I got the code wrong and it should be Radius * 0.99 (some number < 1,0) rather than 1.01. The intent was to avoid invalid geometry in the VRML export. Since IDF does not export graphical arcs or copper traces, the error is somewhat meaningless in IDF but it's sharing code with VRML. In reality you do indeed have some strange geometry; in the case of a 360 degree arc you are in effect defining a larger circle and for <360 degrees you have some cherry-shaped arc.