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Correct, HasAbility is not established until very late, so that everything that might disable that ability can be taken into account, so find something else to test in order to figure out whether that character has that ability or not.
hero.childlives[dPlaFist]
will test for its presence, but if there was ever an archetype added that replaced the level 1 ability of whatever cleric domain you had selected, that would still report that you had the ability. However, unless you want to replace dPlaFist with a copy that adds a Custom tag while present, that's the best you'll be able to do.
HasAbility is not an instruction: "turn this on" - it's a report: "we're active", so assigning the tag means nothing.
Class specials can only be added by classes, custom class abilities, or archetypes. They depend on that linkage to the thing that added them in order to figure out their effective class level. I think you'll need an archetype to handle the "add it if we don't have it" part.
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