The application icon is in the application bundle. But are the document icons there as well? I think that’s what he wants to change.
You may be able to tag files using finder tags based on what you want the icon to be, then use AppleScript (or possibly other tools) to change the icon (as you would via the Get Info window). The ability to change icons is so baked into the Finder and has been for so long that I have to think it’s scriptable.
If this works, it might only stick until you open the file again, in which case Preview would presumably generate a new thumbnail from the contents. It may be possible to have Hazel watch the directory and then replace the icon, either on change, on file close (if that’s possible) or just on a frequent schedule.
Not the cleanest approach, but unless there’s a (hidden?) preference for the automatic preview icons, it may be the best you can get.