Celestial:
If you do try for the directory (i.e *NOT* .DAT file) version of Patch000.dat, you have to make sure that you include CLEAR instructions to the user to set the entire directory to "Deny Write" mode to everyone (including SYSTEM). Check out the other sticky in this forum for details. The only problem is that there is no way for you to do this for the end user, short of buying InstallShield Developer (or writing up a good Mod Manager), so for those people who don't know Windows well, this might be a problem.
I'd actually prefer the directory version of Patch000.dat myself, since it all but eliminates the NPC companion problem, where NPCs do not level because they cannot overwrite the .pro file under the \data\critters directory. As I said in the other post, modding games become a piece of cake under this configuration: Just turn off "Deny Write" in the Patch000.dat directory, make any changes necessary to implement new mod, and turn "Deny Write" back on before playing.
Another advantage to this approach is that you see at one glance which file(s) are being modded, and a quick "fc /B" can give you a list of differences between each mod so that integration of different mods can be done relatively easily....subject to file overlap considerations, of course.