Debatable, they aren't the focus but on their relationship hinges the conflict of the story.

Exactly. If Keine weren't attached/attracted to Mokou, the story would have been much different.

Aside from which, we have pairing tags on stories with much more tenuous connections than this, for instance.

agreed.
And hey,
Its surprising and refreshing to see a pairring being used so subtly and elegantly to spin a story.
Great Doujinshi.
But yeah, if you read between the lines, you can clearly see keine and mokou having something going on, eventhough its not clearly stated.