I've finally completed this quest, and with it the entire "Bartolomeu" storyline. Definitely a fitting finale to the story!
Gauthier Thomassin has to be one of the worst pirates in history - "worst" as in "not very good at it".
First he leads the crew into a mutiny over the disposal of the Aztec throne, thereby missing out on the plunder division which is just about due. To be fair, this isn't as good a haul as some previous ones, we're only splitting 6 million whereas last time we split 10 million. Then he tries to take on the warship carrying the throne and promptly gets himself blown out of the water.
So then we have some set piece dialogs, a bit of "Assassin" style sneaking to rescue Elting, and some "Woodes Rogers" style puzzling in the tunnel, before the big action sequence. Unfortunately game saving is disabled here, but I've got a savegame from the last possible point. First time through, I couldn't get the rifle because I had too much junk in my inventory. The next couple of times, Elting managed to get himself before I got to that point. The next time there was a random crash - yes, these still occasionally happen even with the new "ENGINE.exe". Finally I managed to get through to the mortars, Elting hadn't died, and I managed to hit "F2" and toss a few weapons which had been auto-looted from dead soldiers before Queiroz managed to offer me the rifle. Then I couldn't get it to fire. Fortunately this time Elting had not only managed to survive this far, he also managed to finish off his enemies without my help. We got to set light to the powder store which the governor had proudly shown me earlier, then retired to a safe distance to watch the big bang. Return to Sao Jorge, and Bartolomeu finally has a decent ship.
In due time I figured out why the rifle wouldn't fire. When it is equipped, the game turns into a first person shooter, and I reacted accordingly. Of course the gun won't do much if you're trying to fire by pressing the mouse button. It works a lot better if you press the same key as you would to fire a proper gun...