In the middle of a war, changing her shirt to a red one probably wasn't top of their priorities. She had the authority, everyone called her "captain", so it doesn't really matter much.
In most of your examples, the logical person takes charge. Kira and Worf essentially seem to have parity in rank, so it's down to the particularly situation, and Sisko's orders, for who is in command. In 'Starship Down', Worf is the logical choice, because he is more technically versed in Starfleet operations needed for repairs to the ship. 'Rules' and 'Paradise Lost' reinforces the idea that Worf commands the ship in Sisko's absence.
'Tears' is the only slightly curious one, although it comes soon after 'Change of Heart', when Worf was on the receiving end of a dressing-down from Sisko, and may have been temporarily made subordinate to Kira. Alternatively, in that particular situation, they were in the heat of a battle, and Worf was manning the weapons. Probably best to leave him where he was and let Kira sit in the chair.