That's fine for the most part, but in that case do you really feel that same empathy for these proposed simulations?

Yes.

If all you care about is humans maybe you shouldn't care about these simulations being killed anyway. They're less like us than animals, they have no flesh and weren't born of a mother, why do you care about them just because they make a false imitation of our thoughts?

Because I do - and I don't want to change. (This is the same justification that I have for caring about humans, or myself.)

More importantly though I wasn't talking about human-centrism as a moral issue but a logical one.

It is the logical problem that I reject. There is no inconsistency in being averse to racism but not averse to speciesism.