There are millions of lines of elisp that you've never seen. Emacs is after all the eminently hackable editor. And you're making breaking changes to a core API out of a sense of cleanliness? You've now been made aware of one case where the change is harmful, and your conclusion is "this is the one case where it is harmful". No, it's the first case where it's been detected - and that's because expand-region is widely used by thousands of people - and thankfully it even has tests. People's code is going to break.
You are maintaining an API with many thousands of users. Don't break it. If you must, deprecate it. Introduce save-point, and add "You probably want to use save-point" to the docstring of save-excursion.