My understanding of the OP's concern is this: How you train is how you will fight. I think your analysis is an excellent summary of how any art trains for combat or defense without using up training partners.
I think a punch can be pulled with or without hitting the target. During self-defense drills and other practice, I try really hard not to hit someone in the face or head -- never the neck -- especially since pads are not being worn. Shots to the body are another matter. Depending upon the experience and fitness of the participants, I think a certain amount of contact is to be expected.
Now, when sparring with pads, I'm still holding back on head shots, but there will be contact from time to time because it's free form, because people are trying seize the advantage, etc. Again, I'm less worried about hitting or getting hit in the body because I figure I'm supposed to be able to take some hits now and then.
Whatever I'm doing, I always feel like crap if I hit someone too hard. Hitting a lower belt, or especially a beginner, too hard is the worst feeling in the world for me.
As you suggest, control is always being taught and practised. Ideally, that sense of control, even when confronted with real violence, will serve the practitioner.
