I think the plot was too convoluted as it was. Giving a twist to the natives would have complicated matters further. And I don't think lack of subtitles makes the "natives" voiceless, rather it puts us in the main characters' shoes - of not knowing what's going on.

My main question would be how these tribes are identified in the film. How do we know the filmmakers are portraying the Calingo specifically? Why can't they just be generic island tribe that are cannibals?

As you say, the British and the East India Trading Company aren't portrayed as particularly nice people. Jack Sparrow is out for himself. And when push comes to shove, Elizabeth will do whatever it is to save herself as well. One of the themes of the film is how people can be corrupted.

This of course doesn't excuse racism. And you're right when you say that Hollywood is not the place to look for accurate or flattering portrayals of race or sex or sexuality.

Of course I only have my white male perspective to see this film from. There are certainly other race cliches that do stand out to me, but I am woefully ignorant of the tribes of the Caribbean sea.

Given that the film is also a period piece, it's harder for me to fully accept there's any damage being done by a film whose first job is to entertain, not educate. Also given that the film is basically an homage to all pirate movies that have come before, it's hard to bypass featuring cannibals... just as you can't go past sea monsters and Davey Jones and cursed treasure and damsels in distress.