inertia plays a factor more so in how well someone can take a punch. inertia is resistance to change in velocity. that change in velocity in your face when you get punched dictates how hard your brain shakes inside your skull, which determines how hurt you get (and whether you go unconscious or not). if you're a bigger person with a bigger head, stronger neck muscles, denser skeleton, stronger base, etc, you'll be able to absorb a punch better than someone who is smaller because you can resist the change in velocity better than a smaller person can. it's why combat athletes fight people who are the same weight as them. keeps it fair (on top of the obvious fact that same size people can generate similar levels of force)

they're not able to do them by second nature. they've had to throw the same punches thousands of times since they were little kids to develop the technique they have. it's their job to be able to punch well. practice makes them good.

what you're talking about when you say whipping the punch to make it harder is basically just saying throwing it faster to make it hit harder, which is true. force = mass x acceleration and velocity is a component of acceleration. if you throw the punch with higher velocity, you're making one of the numbers you have to multiply to get your force output bigger, which makes the force itself bigger.