I'm pretty sure the coding will work. Those little white boxes are just that. Little white boxes. The smarts are in the SB-900 to read the boxes. Just a simple binary code. As long as I place the boxes in the right location, should work.
Test was successful. Use white enamel model paint I paint two white squares in the approximately the same location as the Nikon stock TN-A1 filter, and the SB-900 recognized my homemade A1 filter.
Please excuse the quality here. These shoots were made by a coolpix camera:
Your comment about the 16 possible code combinations leaves me wondering. Are there other possible white balance settings they have programmed?
Will take a little work to test. I'll make some simple test strips with all the currently unused codes and see what the camera thinks.
In the meanwhile, do seem to have uncovered a simple way to make your own SB-900 smart filters for pennies on the filter. The only hard part is making the template, unless you have a friend with a nice router...!