The reason we think intelligence is substrate-independent is that the properties we're interested in (the ones we define to constitute "intelligence") do not make reference to any substrate. Can a simulation of a brain design a aeroplane? Yes. Can a simulation of a brain prove Pythagoras' theorem? Yes. Can a simulation of a brain plan strategically in the presence of uncertainty? Yes. These are the properties we mean when we say "intelligence". Under a different definition for "intelligence" that stipulates "composed of neurons" or "looks grey and mushy", intelligence is not substrate-independent. It's just a word game.