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Lawful_g's right about how to remove the class skill, I just wanted to discuss why.
What's happening is that if a variant class sees the NotClassSk tag, it finds the class it's linked to, and deletes that class skill. There's no code looking for NotClassSk outside of a variant class.
linkage[table] links to cleric for a cleric domain because it's being added to a table that's specifically on the Cleric tab - everything on a class tab is specific to that class. (linkage[table] actually exists for everything that a user adds in HL, but in most cases, it'll get you to the same place as the hero transition, so it'd just be extra typing).
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