Honestly, I can see what the writers were doing. I recognize that they’ve made a decision but I’m also electing to ignore it, because it implies that the two of them stay enslaved for the rest of their lives and nope nope nope that is not in any way, shape, or form something I can see James Flint McGraw allowing to happen to either of them. He loves Thomas far too much to allow him to stay a slave, and likewise Thomas loves James far too much to allow that to happen to him either. I’m going to go with “Treasure Island is quite obviously a fabrication/something we’re not meant to take as canon given some of the other changes made to the narrative in s4,” and assume that James and Thomas either escape or are broken out of the plantation by an irate Madi, because there’s also no way she’d allow them to stay there.