How is reflavoring the bandits into pirates invalidating the choice of the PCs? Because I sincerely doubt that the fight is going to be same if it takes place on a forested road with wagons or on board of a ship where one slide effect can push a monster or PC overboard. Reflavoring stuff can have a huge impact on how the players perceive the encounter, or even how it actually runs. Anyway, my players are well aware I reflavor encounters and I happily would direct them to this thread.
As for running a plot-driven campaign, yes, I run one. It is what my players litterally asked me to do. For a player driven campaign the players need to invest a lot more in their characters and the campaign then with plot driven adventures, which costs time and energy in between sessions. Time some of them simply do not want to invest in the game and for which I cannot blame them. We picked the theme of the plot together and they designed their PCs to fit that theme. I don't have to give them an illusion of choice for the bigger choices or plot hooks. Due to how they designed their characters, I know in advance the ones they are going to make. They will not unexpectedly decide to ignore the BBEG, switch sides or decide to start a kingdom. Of course, if they as a group decided they wanted another type of campaign I would go with the flow. I have no big vested interest in the plot beyond a few pages of notes which I have no trouble with discarding if my players prefer something else
Having said that, my campaign is riddled with choices on how they are going to approach a problem. In a way the players know the end destination of the trip, but the choice is in what road to pick. I usually try to add these choices at the end of a session even going so far as to add an encounter to the existing adventure to adjust the pacing. There is no reflavoring necessary since I don't design the encounter until the choice is made. Obviously, DMs bias* is going to impact what is going to happen and I honestly cannot guarantee the players with 100% certainty they would have had a completely different adventure if they had made a different choice - especially not in regards to challenges (beyond obvious impact the PCs powers, skills and abilities have on terrain and environment). Chances are though that it would have taken a different direction.
* The idea that you could somehow avoid DM's bias feels rather idealistic to me. Even if you use random dice rolls to decide the outcome, you decide the odds. Even more, you as a DM describes the world to the players and hence how they perceive that world and what is likely going to happen after they made their choice. If you as a DM have a preference for one thing or another, it is going to show itself even subconsciously in how you describe it. Of course, as a DM I do try to minimize its impact as much as possible within my comfort zone (I hate designing random tables for example).