Ubisoft, and with Far Cry in particular, have realized what their main audience is and it's people that honestly don't give a shit about the greater tone or themes of the story. They just want a backdrop to do this shit in. This even plays into the only central theme that seems to persist in modern Far Cry, the fact that nothing you do matters.
Far Cry 3 - You take down the pirates/slavers, only to leave a murderous tribe in power.
Far Cry 4 - You take down Pagan Min only to have another extremist regime rise up.
Far Cry 5 - You take down Edens Gate, only to have a nuclear war ravage the land you were trying to save.
Far Cry 6 is slightly different though. This isn't a theme presented when you finish the game, but is presented from the very start. As you make your way to Libertad HQ roughly an hour or two into the game, Clara flat out tells you that killing Castillo will not magically fix Yara. That even after he is dead, that factions will be fighting for power, that other countries will get involved, I think she even says it would take at least two generations for any meaningful change to come and that she will not live to see a free/peaceful Yara. Instead, Far Cry 6 adds (or maybe I should say beats in) another layer to the point with it's ending.
You topple the Castillo regime, with Clara dead everyone names Dani the new leader. And yet Dani says he is not a politician, Yara is theirs, don't fuck it up, and walks away. But the fact is we know that they are going to fuck it up, as it's a point Juan, Clara and history itself has shown us time and time again. At the private funeral, Dani admits to Juan and himself what people have been saying throughout the whole game. YOU are a guerilla, YOU enjoyed being a guerilla. It wasn't about Yara, it wasn't about Castillo, it was about YOU having fun.
That's Far Cry. Not some story trying to get a message or theme across. It's about you fighting against a force and having fun while you do it. If you were playing this game to figure out why Castillo did the things he did, if you were playing to find some sort of enlightenment or message or come away with something more than just playing a game, you missed the point.