I could see the argument that Emissary does not belong because it is a pilot: we are getting necessary background information, but it is being presented in such a way that we get a more direct visual record of those events than we would normally. On the other hand, the episode hits key points in Sisko's relationship and his feelings for Jennifer that we never really revisit, even with mirror Jennifer. It's a static part of Sisko's life for the entire series, with mere passing references with old friends.I did also include longer relationships in cases where the audience only experiences the story in the defined parameters of one episode ("The Inner Light", "11:59", "Homestead", maybe "Rejoined" depending on how you look at it). It could definitely go either way, but since Jennifer is dead at this point and their relationship progresses no further beyond "Emissary", it does fit those parameters.
But it is definitely gray, the whole thing is a bit of a subjective exercise in "what is ROTW in a Star Trek context?" and figuring out how to draw those lines -- maybe I'll lob them all off when re-running the list in the future.
I see Prime Jennifer and Mirror Jennifer as distinct and parts of different (though related) stories/relationships (I have "Resurrection" on as a ROTW with MU Bareil, but nothing with Kira & Prime Bareil, for example).
I think where I would particular push back is on the notion that any Romance "Of The Week" should necessarily be vapid or short-lived. However, I think Paradise Syndrome would be no less such an episode if we had seen Kirk married to Miramanee for years and their child lived. Indeed, even though the romance would have been bottled up in the one episode, showing more of the relationship between Kirk and Miramanee would have been seen as overcoming the shortcomings of the genre.