Duncan doesn't aim for a unified ideology because such a thing is impossible even in modern times.
It's best if they argue.
With royal power and the military in his hands, Duncan is not afraid of things getting out of hand. Only when people argue do they begin to question the church, for the church has no theoretical basis to suppress everything.
To be blunt, how many divisions does the Pope have?
If you really push Duncan to the limit, not to mention the reform of polytheism, even Christianity would have to be reformed, with Protestantism appearing over a thousand years early. The church in Britain has always had an independent tradition. If Duncan wishes, the saints here could challenge the church and crown Saint Patrick with a red robe.
Duncan can't outright suppress the church, as it has been spreading for hundreds of years and is deeply rooted in folk beliefs. Forcing the church into a corner would make a slew of saints fight him to the death.
