Not the rule on "every other stage". If you're gonna scold people, being totally wrong may not be a good look.
Obviously there's no reason to criticize the rule on flat stages. Having it on this stage is fairly unusual. Hence the discussion.
It's not remotely unusual to have it on this stage. It is the rule by default, and hilltop/summit finishes are the exception. Race organisers don't have to specify which stages it will be applied on: determining the finish to be a climb does that. I guess that is why flat stages ending in a short sharp climb (to make for a puncheur-friendly stage rather than yet another for a heavyweight sprinter) don't give cat 4 points on the line.
By my reading of the rules, it should apply even where the points line is shortly before the finish line (think of Mt Faron finish in the Classic Var this year, where Lenny Martinez mugged Tobias Johannessen at the end, after the Norwegian mistook the KOM line for the finish line 100m beyond it. That was a 1.1, so not an issue there, but we have seen that type of layout).
I guess that if the organisers wanted the rule to apply here, they could have made the finish a cat 4. Maybe if the rule is not rewritten, we will see that in a number of stages next year.
What is unusual is for it to come into play on a stage like this. As
@Gigs_98 said, not the application that was envisaged when the rule was drafted. I would, though, dispute with him whether it was "stubbornly applied": it is not at the race organisers' discretion, and they would have been open to all sorts of accusations if the rule was ignored when it should not have been.
UCI are usually more keen to react after flaws are exposed than at trying to predict when their rules might be badly written, so expect a re-write of this one at their conference around the time of the World Championships (either road book to identify when it applies, or clearer "unless stage ends with, or has within last 3 km, a categorised climb")
But it undoubtedly was a rule here, so there is no real controversy.