Another theory about Subaru Okiya. This one is about him being Bourbon.
Subaru Okiya would have been Akemi Miyano's boyfriend and a detective student. They separated before she met Shuichi Akai, but Subaru was still in love with her. He felt that Shuichi has taken Akemi away from him. When she was killed, he put all the blame on Akai and decided to avenge her from the man who got her killed. That's why he joined the Black Organization.
Although he is a BO member, he doesn't really have the spirit and is a very nice person to most people. But when confronted to criminals, especially coward ones, the hatred in him surfaces (hatred which made him joined the BO), giving Haibara the strange feeling of a vanishing BO's presence.
"If I had to choose, I'd say black because it is a color that covers things inside me that I don't want known. Well, I hate the color black for the same reason as well."
As a detective and despite having becoming a BO member, he would still have a strong sense of justice and hates criminals (and he wouldn't like at all to be a criminal figure). For the same reason, he doesn't get along with Gin, not even knowing he was the one who killed his loved one.
Knowing that Haibara is Akemi's sister, he acts nicely to her, showing some protective attitude toward her, but she fears him.
Then, who would be Scar Akai ? At first, Gin seems to recognize him as the true Akai. Then, Vermouth appears and reveals something to Gin.
"-Did you get authorization from that person ?
-Yes ! The boss is very cautious. Like a stone bridge, if you strike it too much, it could break.
[...] -It's useless staying here any longer Chianti. We're leaving. Hum ! Always doing things as he pleases ! That bastard irritates me. Someone you wished was only in a novel. A great detective like Sherlock Holmes."
I think Vermouth REALLY is linked one way or another to Scar Akai, thus explaining her strange presence on the scene. But then, why the boss and Vermouth know something even the other members didn't ?
I think the BO wants the FBI to think Scar Akai is the real Akai, with the impostor playing the part admirably. By not telling Gin, Vodka and Chianti until the very last moment, they made sure the FBI think they are really trying to kill him. They probably hope to use him as a spy inside the FBI later.
Whereas Subaru is Bourbon or not, even HE clearly didn't know Scar Akai wasn't the real Akai at first, saying "We're both at fault, 50-50. You should pay more attention to the people around you."
This sentence could also have different meanings. It means clearly that Subaru says to Jodie they are both at fault for having thought Scar Akai was the real Akai, and he tells her to be aware of Scar Akai in the future. But, if my theory is right and Subaru is Bourbon, it could also be a reference to their past relationships: Subaru would have lost Akemi such as Jodie would have lost Shuichi, and they have both lost their loved ones (or at least Jodie thought so for a while). Subaru could feel some empathy toward Jodie, seeing her as much as a victim than him.
Now, Beika. Why would Scar Akai appear near a bank and a department store in Beika ? I think it could have some importance in a future plot. Or maybe it was Vermouth's attempt to make contact with Subaru, knowing full well his hatred for Akai would bring him here.
Then, there is the most important dialogue:
"Remember how there was a robbery at that bank? There was someone I knew in the footage from that robbery, so I was trying to find out if they use that bank. If that person uses it, they must live nearby. I was hoping to run into them.... Well, coincidentally they were also on this floor, but it turned out to be a look-alike, so I didn't say anything. I know that person from a long time ago, so there is no way I would mistake them with a look-alike."
The code could be:
1: There was someone I knew in the footage from the robbery, but it turned out to be a look-alike so I didn't say anything. There is no way I would mistake them with a look-alike.
Translation: I thought I saw Akai in the footage from the robbery, but it turned out to be an impostor. There is no way I would mistake someone else for Akai.
2) They use that bank. They must live nearby. I was hoping to run into them. Coincidentally they were also on this floor. There is no way I would mistake them with a look-alike.
Translation: The Black Organization (the whole organization or just some agents) uses that bank. Their hideout must be nearby. I was hoping to run into them. Coincidentally they were on the same floor than us. There is no way I would mistake one of them for someone else.
Conclusion: Bourbon would be a new agent of the Black Organization because he wants to kill Akai. But he wouldn't get along with most of the other members, more of a loner, and it wouldn't be even sure if he is truly faithful or not to the organization, maybe plotting against it.