That's the plan for the live version.
However due to Brit commander design and modding tools limitations, the only way to implement such changes in a mod is to force the player to trigger those abilities the first time using the commander ability.
For mod-feedback purposes we could make those abilities unlock unit-specific abilities separately when triggered for the first time.
This is just me spit balling an idea. Would it not be possible to make the ability an "always on" (which it would not display) that adds a player upgrade which unlocks an alternate commander passive and the unit's ability.

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