The idea that spellcasting clerics aren't run-on-of-the-mill clergy or run-of-the-mill church militant, they're rare and exceptional individuals like prophets and miracle-workers, has been around for a long time; but I don't think it was ever codified into any flavor text in a D&D rulebook until 5e. (I could very well be wrong — there might have been a bone tossed to the idea in the 3e DMG — but this is my recollection.)
So here's the problem: even if "clerics aren't just priests, they're prophets" is now the WotC party line — and I'm not saying that it is, but it would certainly make sense to have that be the party line, because it's an idea that solves a lot of problems; it's been around as an idea for so long because it's a good explanation as to why, exactly, world-altering clerical magic that should lift any setting out of the Middle Ages is in fact too rare to accomplish that — not everybody is going to toe that line.
Module writers, especially if they're 3rd party, are just going to do whatever they want. They'll just make that NPC bishop or prelate who sends the PCs on quests a high-level cleric, because of course they will. They have no reason to make the NPC a 0-level commoner administrator; in fact, they have an incentive not to do that, because it lessens the chance of a murderhobo PC straight-up ganking that NPC out of the blue for yuks and throwing a wrench into the module's plot.
And then there's legacy content. Old modules follow old conventions. And in 1st edition, in particular — it sticks with us because it's where all the famous adventures that have staying power come from — levels were in fact tied to social station. As you gained levels in cleric, you literally went up through the ranks in the church hierarchy — acolyte, adept, priest, vicar, curate, bishop, lama, patriarch, high priest — so a bishop is specifically a cleric of exactly 6th level in this scheme.
Think about Canon Terjon and Cannoness Y'Dey in The Temple of Elemental Evil: they're 6th level clerics, and they also hold approximately bishop-level ranking within the hierarchy of the Church of St. Cuthbert. And this makes perfect sense for a sword & sorcery world like Greyhawk's Oerth, because it's a dangerous place! Having cushy, noncombatant administrators is a luxury of safe, civilized worlds. But in a place like Hommlet, in the Viscounty of Verbobonc, in the Flanaess? Someone like Terjon or Y'Dey can only be a hierarch of their church because they're a sufficiently-leveled cleric to hold their own!