Generally, at least in the beginning of the period, clerics were definitely in charge of education. By the end of the period we already had a separate "teacher" class which cannot be identified with Christian clergy, at the least. However, if we have an Atheist (or at least a Secularist) religion, it's easy to see that the teachers are mostly responsible for spreading the doctrines of positivism, determinism and belief in progress that characterised 19th and 20th Century Secularism. If so, they would be essentially equivalent to clergy of other religions, so why exactly have two mechanisms?
Yeah, that's how it was in Vicky 2. A lean yet overly abstract approach that I hope will be overhauled in the new game. I can see a couple problems with it, both cosmetic and mechanical.
First of all, with the new Interest Group mechanic, you'd think the clergy would be opposed to secularism and atheism and strive, through campaigning or more direct and violent action, for a more religious society – ideally, for a society dominated by their own religion. An atheist state would end up in a very bizarre situation where it'd have to rely on a hostile social group for public education. I mean, you could create a special kind of 'irreligious' clergy pops supported by the state (unlike the traditional clergy that is being repressed) and focused entirely on teaching and not on promoting religion in any way but a) You might as well just make them a separate pop class called educators at that point, and b) That'd create another weird abstraction because there's no way teachers themselves cannot be religious or support a religious Interest Group.
Clergy was a strange class in Vic2 anyway. They had very little purpose apart from being educators because religion was basically irrelevant in the game. You couldn't interact with religious institutions in any way, there was no state religion (well there technically was but it barely meant anything), there were no sectarian conflicts or other interactions between religious groups, no relation between the number of clergy and the speed at which other pops convert to their religion, etc. The reasoning was, religion played a much smaller role in the 19th century society so there was no need to simulate religions in any significant way.
Which may be true for European countries but not necessarily for other parts of the world. I could totally imagine religious conflicts between Muslim branches in the Middle East or Africa, official persecution of Judaists in the Russian Empire, or even movements opposing Catholicism in the US. With the new Interest Group mechanic, religion may become a major issue in any country's internal politics. You could support one group over another, mediate between hostile denominations, fund religious institutions, or you could just declare yourself an atheist state and persecute all religions equally. Clergy would finally have something to do in the society apart from just bumping literacy.
And with that, you could finally unbind bumping literacy from clergy. I mean, yes, at some point in history, priests were indeed in charge of education. But the 19–20th centuries were the times when they were largely replaced by secular educators, and I believe it'd be nice to have this kind of change represented in a game that is all about societal change.
Buildings are a major mechanic of Victoria 3, if devs' comments are to be believed. They are where pops work and perform their duties. I bet schools will be in the game, but who are they going to be staffed by? The clergy? That'd work for madrasahs and parochial schools but what about general public or private schools? Industrial schools? Universities? Could they also be manned by middle-class professionals like clerks or machinists? Wouldn't that liberate the education system? Have schools, can teach; it's up to you and your internal policies whether it's done by clergymen or secular teachers, or both.
And last but not least, "you have state atheism so pretend your clergy are now irreligious teachers" sounds like a half-arsed handwave. It's like having the player plop down factories by hand and telling them to pretend they have laissez-faire. Wait a second... OH SHI––!
