Interbreeding wouldn't result in specific mtDNAs on "specific islands and even specific populations". This has to be the result of population isolation and I'm guessing long isolation at various locals. Long isolation accounts for the high number of mtDNA mutations not found in other populations.
FWIW Melanesians have the greatest genetic distance from Africans according to Cavalli-Sforza.
Yes--isolation and then rearranging the female lines through raids. It's also interesting to note that Africans have a great amount of genetic diversity.