The death of Captain Flint described in the book doesn't necessarily negate the events that (may of may not have) happened in the show. If Silver's story about the farm was true, there's no reason to suggest Flint didn't later leave for some reason and go on to die in Savannah of alcohol poisoning.
A friend of mine also suggested Flint's ending was rather ambiguous, which I do agree with. I like to think Silver's story was true, but there's certainly points to suggest it wasn't (the birds) and points to suggest it was (sending someone to the farm to make inquiries). In the end, unless the show-runners state one way or the other, which I hope they don't, Flint's fate remains either a mystery, or is decided by each individual viewer's preference.
I wonder if anyone thought the overall ending was too happy? I liked seeing everyone land on their feet because it was the most unexpected way the show could have gone, but it's pretty rare for a drama these days. Certainly rare for a series that got as dark as Black Sails did at times.
There are too many differences between the characters and events shown in Black Sails and the characters and events in Treasure Island.
1. In Treasure Island Israel Hands served as a gunner on the Walrus. In Black Sails he doesn't even touch a cannon.
2. In Treasure Island John Silver was already a pirate before he joined Flint's crew, originally serving under Edward England. In Black Sails he's a merchant sailor.
3. In Treasure Island John Silver's leg was shattered by a cannonball. In Black Sails the leg was smashed by Jenks.
4. In Treasure Island Flint's treasure was so big (silver bars, gold coins, arms) it had to be divided into three piles and buried separately on three different locations on the island. In Black Sails we have one chest of jewels.
5. In Treasure Island the treasure was buried by Flint and six pirates. It took them one week to bury it all. When the treasure was buried, Flint killed them and buried the corpses, except one of them, Allardyce, whom he left unburied with his arms outstretched to serve as a pointer toward the main bulk of the treasure. The whole time Billy Bones and John Silver were on the Walrus and when Flint returned the Walrus sailed away to hunt for even more treasure. In Black Sails in one day the chest was buried, Silver was on the island trying to kill Flint, and the Walrus was destroyed.
6. In Treasure Island Flint draws the treasure map. There is no map in Black Sails.
7. In Treasure Island Flint dies as a pirate from too much rum. Before he dies he gives the treasure map to Billy Bones, his loyal first mate. In Black Sails, Flint willingly goes to a prison (I don't care if it looks like a plantation, it's still a prison) and Billy is Flint's quartermaster who gets demoted and eventually becomes Flint's mortal enemy, ending up stranded on Skeleton Island.
8. In Treasure Island John Silver is a pirate through and through. The only goal in his life is to get his hands on Flint's treasure. In Black Sails he becomes a peace-loving philosopher who doesn't care about the money at all.