You hit a crucial point. Our habits and what we do day after day shapes us as a person and determines who we are. A little I’m sorry every now and then certainly doesn’t hurt, but it can for sure undermine your confidence if used all the time.
I especially like your third point as it turns the whole thing around. Saying “thanks for waiting" instead of “I’m sorry” shows that you appreciate what the other person did.
However, I think it’s important to keep in mind that for some things (like being late), apologizing is the right thing to do. If you messed up, own your mistake and apologize. Then, add in the thanks for waiting. This shows true confidence instead of acting all tough.
By the way, this is an awesome article. Straight to the point, no BS and a lot of examples to act out in your own life.