This type of comment is the hardest to make for me as I know it means redoing a large part of the work from scratch. It would generally be avoided by having quick design reviews before starting to code something difficult or involving sweeping changes. Just highlight how you are going to do it in a few sentences.
On the other hand, letting these kind of things go through usually means you will have to deal with the outcome later, and it will be more painful.
Maybe one way to decide about making this call or not is if you find the submitted version bad enough you are ready to implement the alternative yourself, immediately.
And it happens. With junior devs, or because people are new to the codebase.