Well I finished up some testing with the guilds. You can read the results here.

As for the game being patched, when that happens all of your mod files that have had any changes applied in the patch become out-of-date. You will, however, be able to apply any and all patches without doing anything to the game, modded or not. The patches will only affect the versions of the file that are still packed in the .pack files, as well as any executable code they've changed. We unpack those .pack files to get the text versions that we can edit... but since no one modifies the original pack files that the official updates will affect, you have no conflict at all between mods and patches. To run the updated game, though, you'll have to use the original shortcut and executable the game comes with, disabling any io.file_first or mod usage that you're currently doing. Presumably the modders will work quickly to apply their work to the newly released files, and you should have patch-compatible mod versions in short order after any patch.