Interesting choice for a GIF, why would he specifically pick one that shows a train? The man marked by flames could be Tom.
So what Lafitte depicted as a black ship was just another Sea-Train instead, custom-built for Tom to hide the last road poneglyph, and as a fishmen, he can easily create whirlpools that sink approaching enemies as we saw in Namis Arc when a marine ship came to rescue the Village and was sunk to the bottom by Arlongs Crew.
We also know the last road poneglyph was on Fishmen Island before, so somebody moved it from there. Who could have been trusted enough to just show up there, and take it with him if not a fishmen like Tom that helped the Roger Pirates.
This Cover Story is sus too. "Burning island", huh? Nice hint, Oda. We never saw Tom getting killed by the World Government in exchange for more Information, they could have let him stay alive / work for them. "A Pitch Black Ship" indeed. Double-Agent Tom out there on the Move.