Well, my first reaction to your question is concern. You are attempting to train for something without any real understanding of the methodology. And the fact you have put out there, you are basically changing your body to match the technique, not adapting the technique to your body. A fundamental mistake that will result in injury.
First, if you are kinking your wrist to make contact with 2 knuckles, you will either lose power or injure your wrist. You need the wrist to be supported correctly otherwise it will bend. Energy seeks the path of least resistance, if it can bend the wrist, it will. If it can't it will continue until it finds the weakest outlet, elbow, shoulder etc. This is one of the reasons when you hit correctly you transfer the power without injury to yourself, and when you hit incorrectly, you hurt yourself.
Moral, use good technique.
The harder the object you hit, to more important this becomes. A mitt or a bag has give and absorbs a lot of the energy, makiwara less, a wall much less.
As for your knuckles, your middle knuckle will injure for 2 reasons. One, because force is inversely proportional to the area of contact, meaning if you hit with one knuckle instead of two, it's absorbing double the force. (it's also transferring double the force so that's good). This is easy to demonstrate in person but to give you an idea all you have to do is slap yourself in the chest, then using the same amount of power poke yourself in the chest. Because of the much larger area, the slap doesn't hurt much if at all, where the poke is much less comfortable. Same thing is happening to your middle knuckle when it's out there all by itself.
There are all kinds of ways to toughen up the callous on your knuckles to reduce injury, but in my mind that is trading one 1 injury for another. You can punch sand, or pebbles and be all old school Kung Fu, the makiwara would help as well...but as the previous poster says you should ask your Sensei. Hopefully he knows what he's talking about (many do not sadly).
Another, and IMO more sane approach is the break with your hammer fist or palm heal. The added area of impact and natural padding between the striking surface and the bone will go along way to protect you from injury, and you can still break a lot of stuff.
Undefeated in all of Asia!