No, Sugar babe, you were not able to follow the logic. The Bangsamoro chose Islam. They don't have problem with it. Their problem, it seems, is with the Philippine government who they believe does not have any moral sovereignty over them. The Manila government forfeited that claim when they raped the resources of Mindanao, installed pliant and corrupt leaders like Dimaporo, and failed to deliver on economic equality, thus making regions in Mindanao the poorest in the nation. The entire country paid for that mistake in terms of the longest rebellion in the world today.
At no time in Bangsamoro history were the Spanish, American or Philippine government had full control over them. They joined on their volition to call themselves Filipinos. And if the deal is not fair, they feel free to drop that appelation.
A couple of historical points:
1. The most relevant analogy is Singapore. Singapore chose to join the Federation of Malaya in partnership with Malaysia. The marriage did not work, so Malaysia and Singapore separated as independent nations. Now, Sabah wants out to.
2. There is no such thing as "Kodigo ni Kalantiaw". Did you hear of it in High School? It is cruel and embarassing fake. Check Google. It is at this point where I would have asked you to get a refund from your school, but I will excuse you because the Code of Kalantiaw was a proud and honored part of our history that turned out to be faked. And those absurd death penalties imposed by "Kalantiao" was just part of the sick mind of the faker whom we now know as Jose Marco, who should be ritually shot in Luneta every National History Month. Isn't that funny? The two worst fakers in Philippine History are named similarly: "Marco" for the "Code of Kalantiaw" and "Marcos", the "hero" of Bessang Pass.
http://en.wikipedia.org/wiki/Code_of_Kalantiaw