The GRF copies vehicles by modifying one property each for each original vehicle. The grf I started with (downloaded from the first post in this thread) sets property 07 (load amount) to zero, making all the original vehicles available but carry no cargo (or in the case of aircraft, no passengers).
I had to set at least one property per vehicle to get the copies to appear, so the attached (I hope) grf does the following:
Trains - Set property 25 (user bitmask) to zero.
Road Vehicles - Set property 1C (misc flags) to zero (so none of the original road vehicles can be a tram or use two company colors)
Ships - Set property 17 (misc flags) to zero (so none of the original ships can use two company colors either)
Aircraft - Set property 17 (misc flags) to zero (so none of the original aircraft can be seaplanes... Has anyone ever actually seen a GRF that includes a seaplane?)
n.b. I don't have TTDPATCH or a Windows/DOS machine to run it on, so there is a good chance that this only works with OpenTTD. Tested with SVN r14239. If you encounter any problems please feel free to fix them and post the results
