First, when figuring out force imparted with a punch, a 1" punch could in theory have as much power as an all out swing delivered on the same trajectory simply because maximum force is gennerated in a punch by moving your body weight into the blow, and a 1" punch is just a punch that starts it's motion when the hand is 1" away from the target. In other words you can move your body however you want in the 1" punch, so you can motivate your mass in a forward motion just as in any other punch and thus impart the same (or simular) force.
Second, people's (well people who are in shape) maximum punch speed is usualy limited by the maximum speed their muscle fibers can contract and by how many muscle fibers are recruited. Even though your hand speed does increase through out your range of motion, the rate of acceleration is not as great twards the end of your range of motion as it is when you start the motion. So distance to travle isn't as big of a deal as it may seem.
If the issue is injury of a bone, bones break when they are forced to absorb force.. So when you throw a punch and impact a target, if the target does not absorb the force your hand must. If your soft tissue can't than your bones must. If The target absorbs more force your hand doesn't hurt. If it absorbs less force than you can break something in your hand. How much force is absorbed by your target depends on a lot of things, like what direction and how fast The target is moving, it's mass, how easily it,s structure will yield and what angles your weapon is travaling it's speed and the mechanics of the motion (how much body mass is behind it). I think a break in the hand probably has more to do with these things as well as the specific condition of the bone (that breaks) in question than wheather you use your first two or last three knuckles. I realy don't think there is any statistical information of much use in this debate so for most practical purposes this whole discusion is somewhat pointless, but in the anecdotal case of tyson punching some guy, what specificly broke? How did tyson punch? and does anyone (even tyson?) know wether or not he had an exsisting injury to said bone? (I mean if he fractured it in a fight and than goes and punds a heavy bag 6 days a week than it isn't going to heal properly if at all).
Now the bones of the metacarpus are largest to smallest from 2nd-5th but if you land a blow with three knuckles instead of two than the force should be equaly displaced over the three.. Now of course that depends on the specific anatomy of the individual (wether or not the individual's 4th metacarpal is impacting the target), but from everything I see concerning the bones.. the 4th and 5th together should be able to carry the same load as the 2nd... Now if you hit improperly than that's a whole diffrent argument. I would also point out an improper hit could very well sprain your wrist and leave you in a simular situation. but presumming you hit properly and you have good bone health, than I realy can't see there being much diffrence between a 2 knuckle and 3 knuckle punch, all else being equal.