I am practicing hand knife strikes (e.g. Brachial stun, strike to pectoral muscle, etc.) on a body opponent bag and the bones of my fingers hurt after practice. Should I just keep on doing this (as hand conditioning?) or is my technique wrong (sometimes I hit with the area around the place where finger and palm connect)? Would it be better or worse in real life (combat)?
Your technique may be correct, it may be not perfect. I can't tell you by your question.
The hand, wrist etc need conditioning. For the spear hand, make sure the fingers are a unit, otherwise the middle finger takes all the thrust. Normally it can't take it. Align the three fingers will help.
To train your wrist you could do push-up on the fist. So very shortly you have the wrist in the correct position.
In the hand knife position, do you hit with the fingers, or with the side of your palm? I do the second. So I can bend my fingers, giving me the chance to tighten the meat on the hitting edge.