Yes it is fine. it is a large part of many styles of Kung Fu and you should be using the lower 3 knuckles for the strike. Classic straight punch.
i can't see how punching with the lower three knuckles would be more affective than the upper or frst two
I can see your point about a moving opponent but it is in the style of the punch too. You are either consciencly using the top two or bottom 3 while lining up and judging the punch. For the vertical punch it is the strongest in both punch and the line all the way up the arm. Hundreds of years of Gung Fu cannot have gotten it too wrong.
But in real life when the person/thing you're trying to strike is moving and bobbing to avoid you, connecting only with certain knuckles is almost impossible anyways. :icon_neut
That is where speed and accuracy and a truck load of practice come in. The punch is generally best for the stermum type punch. As for the style of punch it depends on whether you are looping it first to put them off and have to make corrections at the last moment. It is a mental choice that can be changed at any minute. The top two are slightly easy for snap punches and the bottom three tend to be better for the pumelling type punch. And yes someone who is good at evasion will anoy the hell out of you if you have a specific thing in mind for them. Let me know if you are still confused.