The technicals can all be right and the DNA can go wrong. You will be the one to decide this chick's fate - to face a struggle that other chicks don't face, knowing it may not be able to keep up or even get enough to eat for its survival. It's your call, but most of us here would urge a...
Sometimes the humidity level can fall during the latter part of incubation and interfere with development, and the same can happen as a chick hatched by a broody pips and is very slow out of the egg.
I'm afraid there's nothing you can do to make these deformities go right.
The best you can...