The Boss approved the killing of Kogoro right?
I feel like there is something in here. Kogoro (if he was Anokata) might be testing Conan, if he really was Shinichi or he might be luring the FBI out and see if Conan have already made allies with them.
I'm sure Anokata is a very intelligent person and can read people's next move. If he was Kogoro, he probably already knew that Conan would save him (with the soccer ball) so he proceeded with the plan.
But Gin insisted to still kill them both, that's probably why Vermouth tried to stop him. It's probably not part of the plan.
Also what got me is the answer of Vermouth when Gin asked Vermouth if she is somehow related to Kogoro when she tried to stop him. (Remember the pointing the gun scene)
And, we don't know if Gin or Vodka have already met the boss. He probably doesn't trust anyone even if they are high ranking but I believe Vermouth already did meet him.