DC and Marvel don't have 'em, of course. Then, both have grown up over decades accumulating aliens from other planets, magicians hanging out in NYC, supertrained women from all-female utopia with gifts from gods, victims of radioactive spiders or explosions, etc. And even they have a concentration of origins between mutants and the "metagene". The lack's a bit much to handwave in a single novel.
Assuming lots of superheroes and supervillains and all that. That is, your typical superhero universe. A small group has a different logic. It is, in fact, how DC and Marvel started. Particularly DC, where the crossovers came later. Still, it changes the whole texture of the genre to have few, and the world-building ramifications are enormous. A world in which the smallest countries have a dozen and the largest proportionately more, the political balance of power does not change much; in the world where there are a dozen total, whatever country can persuade one to support its policies has an enormous boost over a country that doesn't.
And the metaorigin has to be the right kind. If a ship full of alien children -- different races, perhaps, at a school or being held hostage -- somehow had to land, or crashed, on the earth, and all the children reacted to our sunlight or gravity or something by developing superpowers, it would be SF, however soft. Still more so if you had a bunch of people in powersuits. And urban fantasy with wizards has a lot of Dr. Stranges, but is not superheroic because it's fantasy.
Because on one hand you need the metaorigin to avoid an incoherent ununified mess, but on the other hand, a certain degree of loony randomness is an integral part of the genre. To give you speedsters and flying bricks and wielders of fire or water or earth.
