The truth. šš»
This is going to be long and kind of rambly because I didn't feel like editing it. Also: here be spoilers.
There's something terrible and interesting about the way Miranda is doomed to be a ghost in her own story, the fandom, and Treasure Island (because she's not canonical, despite the connection between BS and TI). She is both haunted by and haunts the narrative; she is largely absent from meta-discussions (I have not seen a SINGLE post about her outside of Tumblr); and has minimal presence in fanvids/fanart/fanfic (Madi suffers from a similar affliction but for different reasons).
It's both frustrating and also so fascinating that both textually and fandom-wise Miranda is most present when she isn't. When people write metas about Flint and grief post s2, and how SilverFlinty it is that John helps him through his depression and suicidal tendencies, or even just bemoan the loss of his hair-- that's all because of her. Her love and loss drive the plot in a very real way that, if you know what to look for, is undeniable but invisible to outsiders. The outline of her (like Thomas) is there.
Miranda changes Flint's path at least four times directly that we know of (seducing him, telling him about Lord Alfred Hamilton's ship's location, the Boston Pardons situation, and persuading him to go to Charles Town). Whether that's acknowledged by fans or not, it's true. After my first rewatch, when I actually knew the full story, I got that Flint cared for her from the beginning. But in case I hadn't, it became explicit and unavoidable after her death. In s3e3, Flint tells Miranda's ghost/hallucination/spirit: "When I lost Thomas, I raged. I was distraught. I wept. But with you, Iām ruined over you." Just because their love was quieter doesn't mean it was less important.
I would personally lean toward describing Flint as Bi if you pressed me to assign him a modern sexuality (rather than thinking of homosexuality/queerness as an act like it often was historically), but I've never been 100% certain of that. (Just like BS' ending. Does John Silver [redact] Flint or [redact] him to [redacted]???). Like a lot of the show, it's open to interpretation.
However, I do think it is disingenuous to point to the one explicit and full sex scene we get between Flint and Miranda and say, "He's clearly gay! Look how bad their sex is." I think the 1705 flashbacks show enough physical chemistry that that isn't a solid argument. Also, I (and others too) read that one bad-sex scene as a reflection of their mutual grief over Thomas. Plus, even if Flint was only sexually/romantically interested in men, he still loves Miranda and is in some kind of involved and mutually fulfilling (at least in the past) (queer platonic) partnership with her. He, Thomas, and Miranda are a trio. BS is full of queer trios: Jack/Anne/Max; Woodes/Eleanor (past / and &) Max; Silver/Madi (/ ? or &?) Flint.
This has been said before, and I'm sure better worded too, but it's also tragic how she never gets to be right and enjoy it. Flint very rarely enjoys being right (and you can debate to what extent he's right about many things; I think the War was entirely justified), but we're clearly meant to root for him. I'd say he morphs into more of an overtly positive figure mid-s3 onwards. Despite the show's tragedy, Flint gets to enjoy a few key and decisive victories. Miranda never does.
When she is arguably most victorious (chewing Peter Ashe a new one in Charles Town), she is killed. Miranda is anointed by her tragic foresight and becomes almost untouchable because of it, morphing into an Icon, patron Saint of Lost Lovers, empty of personhood. And then, in season four, her house burns down, so there aren't even any mementos left. She's erased from the narrative physically and psychologically (who remembers her aside from Flint, Thomas, maybe Silver via proxy, and possibly Abigal Ashe)? Who writes posts about her, draws fanart of her, makes edits and videos with her? She's invisible. She's ignored. She's a ghost.