Honestly, Anon, I don’t think that Silver has ever understood Flint quite as well as he thought he did. I think that there’s a fundamental layer of misunderstanding between them in that Silver believes he earned Flint’s trust through proving himself every bit as intelligent, as cunning, as ruthless as Flint, and in reality I think he earned his trust by simply telling him the truth for once. I’m talking, of course, of the incident with the shark and the conversation they had there. Silver believed he had gotten to Flint there – made progress by demonstrating his cunning to Flint, and I think that what happened in that boat was something else. I think Flint knew that Silver had done what he did. I think he had been holding him at arm’s length precisely because he knew he was being lied to, and I think that when Silver told him the truth, he proved to Flint that they’d finally stopped bullshitting one another. I can’t speak to what anyone else in the fandom believes about what was driving Flint, but I can say that I think Silver misunderstands Flint’s motives quite often, and not just in Season 4. The fact that Silver doesn’t seem to get how he gained Flint’s trust in the first place tells me that he doesn’t actually get the man’s motives – not really, and it creates the foundations of what happens between them in Season 4. I think Silver, interestingly, actually mistakes his own motives in Season 4 in that he attributes what he’s doing to seeing past the darkness that he and Flint have argued about when in fact I’d argue that that is the moment that it, in Flint’s words, cloaked itself in necessity and Long John Silver bought what it was saying to him hook, line, and sinker. He saw Flint acting out of rage and, once again, failed to look beyond to see what was really happening.
Anyway – tl;dr answer is that I have no idea what’s going through the fandom’s heads but I know that Silver does not understand the man he betrayed or the woman he claims to love nearly as well as he thinks he does and it’s part of why he continually hurts them so very badly.