Having Montanez use a Personal flag is still going to cause trouble if you're hostile to Britain. If you're under a false British flag to avoid annoying Bridgetown fort, Montanez is going to attack you because it thinks it's you, i.e. anti-British, and it thinks you're British.
I still remember the time I was playing "Assassin" at the point where you've trailed a French warship to Sao Jorge. It's been repainted and is flying a Personal flag to pretend it's not French. The fort was firing at it. This was because I was hostile to Portugal. So I was under a false flag pretending to be Portuguese, the French ship was under a false flag pretending to be me, and the fort believed both of us.
Really, the scenario as it is has never caused me any serious trouble. Montanez only has 4lb cannons and isn't going to do me much harm before I've dealt with the Animists, and that's only because I intentionally fly a British flag knowing full well what Montanez is going to do. The easy way to avoid trouble is probably to DirectSail from Martinique, where you probably used a French flag to get into St. Pierre. The encounter with Montanez and the Animists should happen straight after "Land Ho", long before you're anywhere near port. Then you teleport to the tavern, talk to the captain, and teleport to the lighthouse where your ship is moored if you're under an anti-British flag. (I actually sailed from Martinique, went to worldmap, exited out of range of any island, and hoisted a British flag. Then I went via worldmap to Barbados, just so I wouldn't end up at the lighthouse because I wanted to sell a couple of ex-Animist ships in Bridgetown shipyard.)
I still remember the time I was playing "Assassin" at the point where you've trailed a French warship to Sao Jorge. It's been repainted and is flying a Personal flag to pretend it's not French. The fort was firing at it. This was because I was hostile to Portugal. So I was under a false flag pretending to be Portuguese, the French ship was under a false flag pretending to be me, and the fort believed both of us.

Really, the scenario as it is has never caused me any serious trouble. Montanez only has 4lb cannons and isn't going to do me much harm before I've dealt with the Animists, and that's only because I intentionally fly a British flag knowing full well what Montanez is going to do. The easy way to avoid trouble is probably to DirectSail from Martinique, where you probably used a French flag to get into St. Pierre. The encounter with Montanez and the Animists should happen straight after "Land Ho", long before you're anywhere near port. Then you teleport to the tavern, talk to the captain, and teleport to the lighthouse where your ship is moored if you're under an anti-British flag. (I actually sailed from Martinique, went to worldmap, exited out of range of any island, and hoisted a British flag. Then I went via worldmap to Barbados, just so I wouldn't end up at the lighthouse because I wanted to sell a couple of ex-Animist ships in Bridgetown shipyard.)