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On my games it seems like a spiritual head of faith will never declare one despite having "Armed Pilgrimages" at the "Organized Warfare" doctrine.
Faiths that have the actual tenet seem to work fine though.
It could just as well be that this was just it not firing due to random chance, hence the question.
When introduced into a save game, all the doctrines are selected.
Therefore, the window is broken by sin and virtue.
Making the choice neutral would solve the problem, but it is not realistic to reform it because of the excessive need for piety costs.