I have a feeling that it's been hard coded into the game, that any clothing, makeup, hair, etc found in the downloads folder is going to get that custom content marker. I guess that leaves modifying the actual game package. I really don't want to have to do that, but, I suppose it would be safe enough as long as I back up the package first.
It's hardcoded that way now, yes. You can dodge this by hucking things into the helpfully provided "overrides" folder in the Pets folder, if it bugs you.