I think that the core problem is the article author saw a change that broke their workflow and didn't investigate any further for why it was made. They simply assumed they knew better and got annoyed that others saw some value in the original change. The very way it is presented in the article - as a change to add a confirmation for register overwrites - is a misunderstanding. The actual purpose of the change was to make C-g, the Emacs "cancel" key, work with register commands. The RET for confirmation was a side-effect, one which the author felt could actually have some value in itself.
Regardless of the reasons for the change, a single author was permitted to commit a change that broke the workflows of potentially thousands of users. And there was no way users could work around it to maintain their previous workflows. That sounds arrogant and annoying.
I think for user facing features it makes more sense to provide new behaviors as opt-in, and go through a longer RFC period. Only if and when the new behavior is widely used and popular, then you flip the switch to default.