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I think that the things that you're discounting are the important factors here. Issues that negatively affect transgender people (bigotry, violence, discrimination. as you said) also affect LGB people and spring from similar causes. It's more of a "stronger together" sort of idea going on. You're right in saying that the specifics aren't the same, but they're similar enough so that it'd make sense to work united on them. (I don't follow the politics of it. These are just my personal thoughts.)