"there's no perceptual difference between a brain running in a computer and on a biological substrate"

Who "perceives" a brain running? What do you mean? Is there some higher order process that can do a "perceptual" comparison between a brain running in the world and an identical brain running in a computer? Is the brain doing this comparison?

It may seem like I'm "nitpicking", but I'm not sure if your statement is even well-defined.