What happened between the time that Dukat seemed to attack Sisko by the runabout and the Defiant gets a message (from Dukat?) about Sisko's whereabouts? Why did he spare Sisko and, more importantly, why did he bother to let the Defiant crew know where he was so that they could save him? That part of the episode didn't make any sense to me. Did it confuse anybody else?
That's what I thought. It's just that the editing was kind of strange on that one particular scene. So, I guess that Dukat escaped via the Runabout and left Sisko on the planet -but then contacted the Defiant so that they knew where to find him (Sisko)?
He wanted to face him again. Or it was part of the Prophets' plan, so that their Emissary (,i.e. Sisko) will defeat the Pah Wraiths' Emissary (,i.e. Dukat) This is essentially what happened at the end of What You Leave Behind, evidently.