Weird. They show up for me.
Obviously I have to check that you've got the mod enabled.
If it is...
If the mod is enabled but somehow not doing anything, you can tell because the "Natural Pet" class does not show up in any non-beastkin's class selection, locked or otherwise. That's probably the easiest way to tell, because if the mod is working correctly, a human master, for instance, would have Natural in the locked section, like it does on my end.
Is it a problem with every guild? Because I did give every guild at least one class.
Do you have any other mods that affect guild shop inventories? If so, where in your load order is my mod?