Maybe an orc witch-doctor (or whatever) had access to a slightly different set of spells from a standard priest, or a different weapon selection. It has different mechanics because it's modeling a different entity. There's still exactly one true way to model each distinct character.
Great example.
The orc witch doctor didn't use the PC rules. It had an extra 1d4 hit dice for each level of priest it took and still used the monster attack rules rather than the priests'.
Most of the bodyguards and warriors and such just gained a bonus hit points and fought as a slightly tougher monster. Which 5e is actually fairly close to since it works a little like this, adjusting monsters with a couple modifications but otherwise using the existing statblock.
So that's the entire 2E era and 3E era which followed this rule. It's a period of twenty years which, barring 4E as a failed experiment, continues right up to the modern day.
Adding class levels to monsters and challenging NPCs with class levels was always rather vestigial in 2e. Most NPCs were 0-level commoners. You could have fighter and mage NPCs but there wasn't really any rules support or advice.
And the xp calculation rules in the DMG really didn't reflect the challenge of a creature: a level 3 mage was worth more xp than a level 3 fighter.
Even then there was a lot more fudging and customization, as the rules were less codified. You could just add a hit dice or extra power.
Of course... you could handwave things in 3e as well. Need a slightly higher CR monster? Give it a couple extra HD and a bonus feat. Bam. Basically just applying a homebrew template. So long as it's done in advance and full xp is awarded it's not "cheating".
And heck, even Pathfinder is moving away from using the full PC rules for monsters. They introduced 4e style monster rules for
Pathfinder Unchained.
Using full PC rules for monsters is problematic. Monsters don't need feats for special abilities. And they don't need to use the same math as PCs, gaining attack bonuses and save bonuses based on their Hit Dice. That doesn't work. The requirements of the game mean that monsters should be hit more often and take more damage than PCs.
To use your parlance, once of the "failed experiments" of 3e was 0-Hit Dice monsters like orcs advancing as PCs. Because orcs and such needed special rules content, which meant feats and prestige classes that were NPC specific. Which was odd. And they still needed to be balanced as PC options. But monster balance and PC balance are not the same.
Giving a PC the ability to raise the dead once a short rest would be crazy good, but a hostile monster with the ability would be fine since it would only be usable once in a fight before it dies. The difference between recharging on a short rest or a long rest means nothing to a monster. And they don't need to worry about saving spells to last an entire day.
Similarly, many PC abilities are useless for monsters. Especially exploration based ones. A monster has no use for bardic Song of Rest.
Divorcing NPC powers from PC powers means you can have the orc Eye of Gruumsh do Gruumshy things without a prestige class, that are balanced for a monster. And it also means the king NPC can have king-based powers related to commanding guards and granting attacks or even legendary actions. Without having to design a "king" prestige class, "royalty" template, or "Hail to the King, Baby" feat at the same time.
And PCs gain a new ability each level, because a single person is managing just that character. But a DM running an enemy party needs to keep track of all the abilities of a potential enemy party, which is unnecessarily complex.
This is not a theoretical problem: I'm running
Madness at Gardmore Abbey where one of the opponents is a five-man band of evil adventurers. That would be hellish in 3e/PF. Especially since 5/6ths of the abilities won't be used in the 4 rounds the rivals will be on the scene.
And
if I decide to design those NPCs by hand, I'm not creating a full PC with stat increases or feats and the like. I can just make up the numbers and abilities, taking inspiration from a couple token signature PC abilities so the NPC feels like they have class levels, without copying the exact rules verbatim. I can give out some extra Hit Dice, adjust the ability scores, not pay attention to saves and skill proficiencies, and not worry about a background that is wholly irrelevant.
BUT if you
want to stat up an NPC using full PC rules just like in 3e,
you still can. That's still a thing. Not only is there nothings stopping you, but the rules for doing so are in the DMG. That's just not how they're presenting characters and NPCs in the book.