I mean, I think you’re trying to join together things that are related but perhaps not really the same.
As @cthawley pointed out, the plunder of Dombey’s collections involved one colonial power taking collections made by…another colonial power. (Incidentally, more recent authors, e.g., Ochoa in “The Potatoes of South America”, p. 704, suggest that the collections, which were not Dombey’s alone but those of his collaborators Ruiz and Pavon, were subsequently redeemed by the Spanish government when the captured ship was sold at Lisbon. The assertion about the British Museum keeping them seems to derive from Appletons’ Cyclopædia, which has some issues with veracity.)
In general, in the New World, the initial flux of colonial plundering preceded either colonizers or colonized having really systematic natural history collections; I presume the more prosperous civilizations had their equivalent of trophy collections or Wunderkammers to be carried off, but I wouldn’t expect such artifacts to be well-curated or -preserved solely on the basis of scientific interest (rather than value as treasure, art, etc.) I could maybe imagine opportunities for such plunder in the later European colonization of parts of Asia (e.g., the piecemeal annexation of the empires of the Indian subcontinent) but I don’t actually know of any cases where something that was recognizably a scientific collection in a colonized polity was carried off wholesale by the colonizer.
My general impression is that natural history collections from colonies tended to be assembled piecewise, often (though) not always by private individuals, and through something much closer to legitimate commerce than plunder. It’s more difficult to make an argument for repatriating those than for something like the Elgin Marbles. The ethical issues here have usually had less to do with the possession of specific, individual artifacts than the general idea that the colonizers obtained very valuable biological materials and knowledge of their use from the colonized without offering compensation proportionate to their value, generally summarized as “biopiracy”. (Which does connect us with Dombey and the Ruiz and Pavon expedition again; they were sent out to Peru in part to make a systematic investigation of Cinchona, whose value in producing quinine was already understood.)