That's just my point: NPCs 'built' differently than PCs means by default that one or the other does not fit the story.
Why does the master village black smith or sage have massively more hit points than the apprentice?
Why does the sage have more hp, weapons, and armor, and BAB than the spellcaster?
Should the 20th level sage be able to annihilate a 5th level fighter in combat? (20d6 hp and +15/+10/+5 ?)
Does an NPC elf wizard need to go adventuring to level or could they have studied for centuries?
I'm pretty good with the PCs being able to get everything NPCs have. I think the other way around is trying to force a story that doesn't make sense.