In New 52, Kon-El (Superboy) has the power of tactile telekinesis (in a far more powerful form than earlier incarnations). This is explained as Kon-El being a clone containing DNA from Superman, Lois Lane, and most importantly, Jon-El (Jon Lane Kent), the son of Superman and Lois Lane from an alternative future timeline. Jon-El was a alien-human hybrid who possessed tactile telekinesis.
So that explains why Kon-El has TTK in New 52. But that just moves the question to, why does Jon-El possess TTK? It isn't a Kryptonian or human inherent power. And while it could be "hand-waved" as being "because he's a hybrid", which lead to strange genetic interactions, TTK as a result of blending Kryptonian and human does not really follow intuitively.
Does anyone know of any justification from the comics or other sources? I am mainly concerned about "in-world" explanations rather than real-world brainstorming at DC, but any relevant information could be interesting.