What about to extend the door further down with a piece of plastic (or carbon) to cover the lower part of the door sills?
Like a flexible door sweep that came down from the bottom of the door and met the edge of the door sill. You wouldn't see it unless you bent down and looked under the door. The door flexes independently from the sill so it would eventually rub the paint off the sill but you could probably prevent that with a piece of clear plastic low-friction tape. I think part of the problem is some of the mud and rocks come from up higher. anything that goes through the crack between the door and the body ends up down on the door sill. VFX maybe you can show us what you did so we could make suggestions, improve on it, not repeat what didn't work, etc.