Hey, as I see it, why NOT give NPC heroes powers and power levels not available to PC ones? The background text for a lot of the contacts makes quite a few of them low-levelled supers with funky powers, or retired ones. Atlas himself had super-growth... it adds to the colour of the game and makes it closer to the comics for powers they either can't yet do in the game (growth, shapechange), or which they don't have to balance (signatures, SVs) to be done this way.
Archetypes and power sets are artificial constructs - it's actually nice to know that the "real" world Paragon is set in is not limited by what player characters have available. (Also gives them a lot of scope to introduce new stuff later on).
Also... when running my Champions campaigns, my characters were never the *most* powerful supers in the world. I always made sure there were a few very tough NPC heroes that could hand them their butts if needs be. Always good design to do this.