It’s because they aren’t small chapels. They’re full fledged churches. When building a church they’re meant to be an end-game buildings like longhouses. In SAELIG churches are owned by the greater catholic church, rather than any individual like in The Guild. Which is why the abbot position exists, to allow the player to work and run the church in town. Indeed if there was going to be a cheaper form of church it would be a small chapel, but I’m not certain how this would fit into things.