Some of the major corrections are already in the thesis
Consider that if your examiners have asked you to add things that were already there, then either (a) they didn't read the thesis very well, or (b) those things that were already there were not clear or obvious. In the case of (b), you want to improve that.

You could reply to "defend" things as they are - but be very sure of your ground before doing so, and expect that the examiners might respond "change it anyway". Unless there is a good scientific reason not to do the changes, I wouldn't bother - as your supervisor said, just swallow your pride, and do what they've asked. While annoying, it'll be less trouble for you, and also not risk annoying people you might want to work with in future.