Rules text is still pending for this, so don't expect too much from the post, but I finally got around to whipping up a mock-up of an affinity tree in action.
This is a relatively complicated one, in the sense that it has a lot of possible ranks, but not necessarily in terms of how they interact.
The Church of the Unsung God is a faction in the Othenar setting, and is very influential on the continent of Halor.
Its structure is somewhat inspired by the concept of monasticism, but each follower of the Church of the Unsung God may actually worship any of a number of deities within an approved pantheon; some of these are the same as can be found on Othenar and Roltam, but many are worshiped only in Halor.
In this sense, most characters in the Church of the Unsung God also have another deity's worship, and rising in devotion is a requirement of the Elder tree and any of its successors.
Ascetics and flagellants are not necessarily worshipers of any particular god, and make up the secular branch of the church; they serve the whole pantheon in an abstract sense.
One of the ideas in this setup is that you can have characters who belong to even the highest ranks in every campaign, as an Ecclesiarch is simply the highest-ranked priest of a particular deity, while Hierophants are simply particularly potent followers of the gods who have advanced to an appropriate rank and then demonstrated a miracle (while mystics do the same thing, but can come from any of the lower ranks).
Characters move up the ranks when they meet requirements (e.g. a militant must have a certain martial prowess, a priest must have a certain rank in a faith, etc.), and each unlock some resources of the organization; be it the mystical power generated by the flagellants' sacrifices or the manpower of the institution (or just being granted the privileges of belonging to the Church, which wields near unquestioned levels of influence in Halor).
Obviously there's a lot of stuff to fluff in further, but I think this is a good starting point and demonstrates the system well.