Looking at current crashes, I think JBeams should have a 3D and Polygon factor. The 3D factor would mean that JBeams should have a value that allows you to interact with them from within a certain radius instead of just hard collision on the spot. It could possible help with the clipping between parts. The polygon factor would be a feature that made sure points on JBeams wouldn't run through the center of formed polygons in the other; also a clipping helper.
Nodes have a thickness for collision and self collision defined in the main jbeam. This value can be changed. This is exactly analogous to your 3d idea. Your polygon factor sounds exactly like collision triangles, which I believe are already enabled for collision with other jbeam'd structures and collision meshes, but not self collision, due to processing requirements? A clipping helper sounds pretty vague. One can use support beams, which only resist compression, to help make sure bumpers don't clip past the fascia for example.
