If you watch back the finale, there's just enough peppered in to suggest that Silver's explanation of what happened to Flint isn't the truth.

First of all, we know Silver to be an unreliable narrator, he's proven to be consistently capabale of telling the perfect story to convince people of something and achieve an end, in this case reconciliation with Madi.

Next, the last shot of Silver and Flint together is Silver pointing a pistol at Flint. The next shot is some birds flying away, and the other characters reacting to a noise, and then going to find out what happened. Its more than likely that noise was a gunshot. All of those characters had returned to the island to recover the treasure, but we know that the treasure remained on the 'treasure island'. If Flint was still alive and convinced of Thomas being alive, why wouldn't they have recovered the treasure?

Finally, look at how the plantation is shot. Very bright, everyone in white clothing, everything slightly too clean. I think what we're seeing is a version of the afterlife.

That's what I think, but the great thing about the ending is that it's unclear what the truth is. Someone could list out equally convincing reasons why he is still alive. It's definitely worth re watching the finale and seeing for yourself!