Great OP!
I think a reason why this isn't focused on about so much (on top of the lack of diversity within games media in general) is that Naughty Dog crafts their stories so that every aspect of it 'makes sense.' Outside of the 'brute' boss fight they don't generally put characters in who don't serve a crucial purpose in the story, and since both stories are pretty much based around "people dying to further a white person's character," that means it 'makes sense' for the black side characters to die. In general there's also the whole "TLoU's world is shit and humans are bad!" thing that is often brought out to justify literally anything bad within the universe. In the end people can justify the problem to themselves because "it makes sense."
However what this whole argument ignores is that fiction never requires anything. Simply crafting your story so that it can't be easily 'torn down' with 'facts and logics' does not justify the story itself. Sure, Isaac dying makes sense for Abby-and-crew's character development, and it fits the game's themes at that point, but he still died because Naughty Dog deemed it as such. Similarly, Tommy, a white guy, survives being shot in the head because Naughty Dog needed him alive for a thematic and functional purpose in Ellie's story.
That boss fight, though. There's no possible way anyone can excuse or even attempt to explain that in anywhere near good faith. The guy doesn't serve a gameplay purpose, a story purpose, or a thematic purpose; he's literally just there to give Abby a scary boss fight similar to the Boomer in Ellie's Day 3. Which itself is strange because the game literally goes straight into the big climactic boss fight with Ellie.