hmmm, wow, because there are too much posts, so I wont quote them on by one, I'm gonna make a quick counter:
1. Why BB has 3 heads in his flag?
Well, there are plenty much speculation in here, but I think the best candidate is Past, Present, Future. Or maybe just a symbol from Blackbeard's origin himself that consists of 3 persons in OP world; Edward Newgate, Marshall D. Teach, and Thatch. Edward, Teach, and Thatch are the same Blackbeard in real life.
2. What caused Shank's scar?
There are too many possibilities too, fingernails would be the best bet. If that was a Cerberus claw, Shanks will know for sure. And look at this one:
http://www.onemanga.com/One_Piece/467/02/
What can causes that hole in the wall? If we dont know Zoro was battling Ryuuma, we will take that as caused some cannon or some beam. How in the hell a sword can make that kind of hole? So we shouldn't be sure about Shanks scar too.
3. If it is not Cerberus, why BB didnt steal any fruit he encounter?
I am pretty sure for this, there's a limit for how many powers he can take. If it unlimited, then it will be too imba. It would be something like Dofla can control all shichibukais with his ability.
4. If it is not Cerberus, and OK, BB has a limit, so why he didnt steal Ace's or Magellan's, it would too stupid for BB not to take the ability to pass bullets with fire logia?
I am not too sure for this, but I'll say that because Yami Yami and Mera Mera are both logia type, and I think he can only manages 1 of each type, so he choose Gura Gura over Doku Doku. So, maybe he can stores only 3 powers at max, not because of 3 heads, but because there are 3 types of DF.
5. Why BB doesnt steal WB when in contact with him?
Maybe because WB didnt die yet, or maybe requiring some special trick that was hidden under that black cloth.
6. Why BB doesnt explode when he has more than 1 DF powers?
Maybe because he didnt ate them, but only absorbs it, so he still only have 1 DF in him, Yami Yami no Mi, but 2 DF powers. If the thing that allows him to do so is Cerberus fruit, it would make no senses, because Cerberus's body is still count as 1, except if Cerberus's stomach is in each of its head.