Several years back, a buddy modified the rear interior panels on his car with some 1x4s, plywood, bondo and this spray texture bodyshops used to match the texture on some rocker panels that is painted over. After we sprayed the texture, we used some sandpaper to knock down the peaks. It matched pretty decent, but it's not perfect, it doesn't replicate the 'wormy' look of the factory embossing.
I have the same problem, except I have holes in the front and rear of the doors. Plus the holes go up where the edge raises up to the removable part of the rood panel. Currently aside from door replacement, I feel my two options both involve welding up the hole with a patch, possibly cut from a rusted out door with bad skins (I'm not looking forward to forming them up by hand) and either getting rid of the embossing throughout, or covering the doors and rear panels with vinyl/leather. I guess another option would be to use the texture I mentioned above, but redo the whole door and the rear panels with it so it all matches. I'm leaning towards eliminating the embossing.