I like the idea.
In my opinion, when deities are actually implemented (and hopefully the 'mystic' position), the entire scene should follow a similar example of:
Dwarves who share the same deity (deities) would collaborate and form their own cult, or religious group. This of course, would result in many different groups.
The leaders of these individual cults are chosen by the members of the cult, instead of the player.
When the player intends to choose the 'mystic' (Bishop ?) for their fortress, they are presented with a list of all the current fortress cult leaders. The chosen leader has their faith reformed and chosen as the fortress' preference (icon ?).
This clearly would create some disputes (as all good religious interaction does) leading into situations where some political muscle may be induced.
Two separate cults/faiths may collaborate and be reformed as a single faith if the chosen mystic expresses religious favour for both groups, creating a new pantheon.
The way I see it, deities which do exist must be surrounded with random 'made-up' deities (leading to religious wars to remove these false deities?) as not much would happen if two war-gods constantly swing the favour of battle back and forth for an eternity.
Clear lines should be put into place as to which deities belong into which faith. (However a single deity may belong to multiple faiths, in reference to the collaboration of faiths).
On the topic of false deities, mystics which are aware they represent a non-existent god (as they may have made this deity to gain political control) would mandate things in the name of their god for their own personal benefit.