This is my 2 cents on why I think punching with the lower knuckles might be beter then the upper knuckles-
First of all, the structure with the arm and its bones are more consistant, providing strength and force behind the fist. The three lower knuckles sort of line up as well, dispersing the energy that is absorbed more equally through all three.
In any sort of confrontation, you may risk breaking something, that is just a fact of life, but conditioning can help.

"try not, do or do not. There is no try."