Making Habanero Jelly - Safety and Preventing Spoilage
In terms of killing pathogens, it is a belt and suspenders thing.  

The additional processing ensures that any pathogens that entered the jars while you were filling them are killed.



More importantly, as Jefromi has reminded us, the additional boiling with the assembled and lidded jars causes the header air to heat up, expanding in volume and raising the pressure, and so some of the air will bubble out past the seal.  When the jars are cooled, the header air also cools, creating a partial vacuum, and pulling the lid down against the jar.  This is what makes the permanent seal--the ring is only there to hold the lid in place long enough for the processing.

So the processing is necessary to seal the jars, even if the food is already rendered perfectly safe from pathogens.

For more information on canning safety, see NCHFP's processing guide.