This is in the same way that the headquarters of the Anglican church isn't London. Perfectly reasonable.
This is quite an interesting subject. From what I remember from C:I, the rank-and-file priests are known as Pontifex - Mundanus for a diocese on x/y/z planet, Terra for a diocese on Earth, and Astra for spaceborne chapels.
Then you also have Cardinals, though there is no mention of Bishops. The big question to answer is how closely do the regional divisions of the Ministorum follow the administrative divisions of the Imperium?
Neither do I, thats why I started this thread. I 'd say that unless its a total back water world you probably will end up having a deacon, especially if theres a large congregation to minister to. And if the world is in a different sub sector to the one with the cardinal world, you are going to want to have high ranking priests around so they can enforce the will of the church more effectively. Thats what I think
Around the Imperium, you have millions and millions of shrines. Each shrine is the center of a parish, which is kept by a preacher. Over the preacher, you have the Pontifex, whose authority stretches over several parishes. There are different kinds of Pontifexes, depending on their responsibility. Pontifex Urba (religious overlord of a city), Pontifex Astra (space craft and space stations), Pontifex Mundi (entire worlds), and so forth.
Over the Pontifexes you have Cardinals. There are thousands of Cardinals in the Imperium. You have Cardinals Palatine (working in the palace on earth), Cardinals Terran (working in dioceses on earth), and Cardinals Astral (working in dioceses elsewhere in the Imperium).
Ecclessiarch - Imperium Cardinal - Diocese (usually hundreds or thousands of worlds) Pontifex Mundi - World Pontifex - A group of parishes Preacher - Single parish.
Of course, you can add a few more in there. Pontifex Regionalis, and so on.
In other words, no deacons. But definitely a Pontifex Mundi, whether your backwater world has only a single shrine, or thousands of them. And this Pontifex Mundi would be under the influence of the Cardinal Astra on Dorvastor.
Note: All of the above comes from Codex Imperialis, except Pontifex Regionalis (which I coined for the Tryphon SR). Minister mentioned deacons and arch-deacons, but I've never heard mention of those in the fluff, and I don't really see the point in inventing a lot of extra titles when GW has set up a rather flexible system. What's the point in creating a rank called 'Cardinal Primus' when you already have the 'Cardinal Astra', for example.