Disputed territorial claims in academic submissions
Definitely point this out. The whole point of soliciting a review is to identify issues in the paper. You should not assume the editor knows the map on page 7 is inappropriate, just like you shouldn’t assume they are aware that step 5 of the methodology is unsound. The editor may choose to ignore your comment, but that is up to them. They should not be annoyed by a legitimate comment like this.

There is no justification for using scientific articles to advance territorial claims. If a political map is included, it should be clear when borders are disputed -- it's factually inaccurate to only present one claim. And one also questions why a political map is needed in the paper.