This is a structure that re-adjusts at the necessity of plot.
In "Paradise Lost," Worf commands the Defiant even though Kira is aboard. Even though Kira was clearly left in command of DS9 when Sisko and Odo left for Earth.
In "Rules of Engagement," Worf commanded the Defiant while Kira was aboard.
In "Starship Down," Worf was left in command on the bridge, with Kira sitting with Dax in the rear of the bridge. Later, Worf ordered Kira to tend to Sisko while he went below to the engine room to regain control.
In "Sons of Mogh," Sisko assigns Kira to command the Defiant to investigate unusual Klingon activity, she asks if she should take Worf. Sisko refuses, but it would have put Worf under Kira's command.
Yet in "Tears of the Prophets," when Sisko is drained by the Pah-Wraith attack on the Wormhole, Kira takes command and Worf says nothing. She looks to him for his opinion on O'Brien's plan to destroy the power source of the orbital weapon platforms, but Kira was clearly in command.
It depends on the episode or the season. Season 4 they were making a bigger showing of Worf being a command officer, they backed off from that in later seasons.
Is it perhaps not more telling that in Shadows and Symbols, neither Kira nor Worf uses the Defiant? Of course, Kira couldn't organize a Bajoran opposition to the Romulans from the Defiant, but clearly Worf didn't get to take it to put Jadzia into Stovokor. Neither may do with it as he or she pleases--not like a Kirk, Picard, Sisko, Janeway or Archer.