Extras were not below enlightened mortals. It was, in fact, possible to be both at the same time. Merely having access to Essence channeling was not enough to make you a Not Extra. A pack of Blood Apes attacking your party were as much Extras as a pack of brigands, just with higher base stats. A group of Enlightened Grass Ninja may be elite mooks, but they were still mooks and the rules would treat them as such regardless of how many Charms they could use.
Heroic was not a distinction of power level, but a distinction of importance. A heroic character was a Named Character, one whose personality and choices mattered and who would get a speaking part. Again, this was unrelated to their ability to use or not use Essence.
Vanilla mortal was a third kind of distinction, one that meant the character wasn’t unimportant enough to be considered an extra but also not important enough to be considered heroic. Thus while they got full health levels, they couldn’t stunt since they were GM-controlled characters not meant to stunt or gain a benefit. They are recurring characters the players may care about enough that you want to apply the full rules of the setting to, but not important enough to justify fleshing them out that much.
Characters could even change roles between these three states as the game progressed. In the early game you might consider a Blood Ape a fully heroic character, especially if you are playing a game with a prelude pre-Exaltation or a low tier Dragonblooded campaign but as the game (and the PCs) progressed in power most you would encounter would become Extras.
Later into 2nd edition, some of the rules began to treat these as proper distinctions rather than storytelling tools for the GM. Charms and effects began to differentiate between them and suddenly the difference between them mattered a hell of a lot more. This was a problem with those mechanics being terrible, not with the rules for extras and heroic characters being broken. You suddenly had magical abilities which were explicitly in setting effecting people in a way that was meta-narrative level. It’s like Charms that keyed off of Stunts, which was and remains a terrible idea. Stunts (and extras and heroic characters) are gameplay-level concepts that should not be incorporated into the narrative level as things characters can consciously choose to be.