Okay. I've figured it. There are two mod folders now since the Aspyr update.
This is the first one, located in call4.app/contents/mods. It contains ModWarfare which comes with the game and works fine.
This is the 2nd one, located in $HOME/library/application support/call of duty 4/mods. This is where the 3rd party mods go, and the mods in here appear to show up on the mods list ingame. This is where you should put your mod.
If you have messed up your directories by following my instructions for when Call of Duty 4 didn't support mods, I apologise and can only advise you to delete the app, the call of duty 4 folder in your library folder and any folders you created while following my instruction and download the game again.

This is the first one, located in call4.app/contents/mods. It contains ModWarfare which comes with the game and works fine.

This is the 2nd one, located in $HOME/library/application support/call of duty 4/mods. This is where the 3rd party mods go, and the mods in here appear to show up on the mods list ingame. This is where you should put your mod.
If you have messed up your directories by following my instructions for when Call of Duty 4 didn't support mods, I apologise and can only advise you to delete the app, the call of duty 4 folder in your library folder and any folders you created while following my instruction and download the game again.