You're begging the question. We don't agree with the premise that it invalidates the setting, so the question has no meaning. PCs can be exceptional. They're literally 1 in a million. Billion. You disagree, but that's all it is.
Sounds like you're looking at a setting where a) the PCs are the only adventurers in existence and b) you're planning on zero PC lethality and-or turnover during the campaign. In this extremely unusual case, the PCs can be as ridiculous as you like.
Otherwise - as in just about every campaign going - when some of them die, or retire by player's choice, or get tossed out of the party, etc. and need to be replaced, where do those replacements come from? Oh, look, the replacements were out there in the setting all along - which by extension means there's others still out there; and bang goes the PCs-are-unique argument.
So, now we know there's more adventurers out there than just the PCs, how do we seamlessly fit them into the setting along with the PCs? By making them all work just like PCs. From there, it's a short and easy step to making non-adventuring levelled NPCs (e.g. lab mages or stay-at-home clerics) also use the PC chassis.
Where do commoners fit in? Well, again barring specific campaign conceits e.g. the PCs were born as children of prophecy etc., one has to assume the PCs more or less grew up as ordinary people within their cultures. Some editions show the mechanical gap or steps between commoner and 1st-level better than others (e.g. 1e has rules for 0th level; 4e has a huge gap completely ignored by RAW that I know of); but at some point every levelled entity in the setting has mechanically crossed that gap. In short: they all came from the same roots.
And those "same roots" are mechanically defined, for Humans anyway, as a 3-18 bell curve over 6 stats. Sheer gamism pushes some toward using point-buy or fixed arrays for PC stat generation; but as none of those methods ever produces anything that can't be achieved by rolling they for these purposes can be ignored.
Throw all that in with the general idea of every setting-population guide I've ever seen indicating that levelled entities are FAR more common than 1/1000000 and you've got more than enough reason to want to integrate PCs and NPCs into the same system.