I don't think it is precise to say that she only has authority on DS9 and the Defiant. Rather, she has authority only through her position on DS9 and the Defiant. Indeed, when Sisko is affected by the closing of the Wormhole, Kira takes over the command of the Defiant. There is no indication that when she did, the Defiant surrendered its lead role in the assault. Quite to the contrary, it appears to continue to lead the Federation efforts to destroy the weapons platforms.