This is missing a key feature of substrate dependence, namely the role of time in the universe. What is implicit in the substrate, is that it exists in the universe. By existing in the universe, it must “flow” through time. And it is this connection to time that is key to its role in consciousness.
Take the standard thought experiment of a simulated digital mind. Is this mind conscious? Well here is the thing about “digital existence”: it lies outside of time. You can run the simulation at 1x speed or 1000x speed, but it makes no difference to the simulated mind, as long as it is isolated from the external world. Even if it was connected to the external world, the fact that it is digital in nature means that save states are possible and there is no longer a linear world line that the digital mind can follow.
And this is why substrate dependence is crucial: everything in the physical world must flow in time, and there is no “going back”. That is, you cannot copy the state of the conscious being, which would be akin to time travel. Digital minds lie outside of time.
So how do we address the fading qualia argument? Well the entire argument falls apart at step one: namely they would be functionally equivalent. Nonsense, they are not equivalent for the most important feature: for something to be digital means perfect knowledge of the state. Perfect knowledge of the state is not a feature of base reality, but is an abstraction layer that lies in a Platonic realm. Having digital neurons is equivalent to the statement that time travel is possible from a subjective point of view.
Of course, this has no bearing on whether or not these minds can act on the world, just that they would not experience time or have subjective experience.
This feels similar to a gauge transformation in physics, where there seems to be an extra degree of freedom that cannot be eliminated. But even within the same mind there is still a problem with qualia: Take the visual field for example. Imagine reflecting your visual field as in a mirror. Would anything change in the external world? I would argue this would also be a perfectly viable mapping of the external world to phenomenal states, and yet, it would seem to imply that the reflected visual field is isomorphic to the original field. It would seem that this experiment can be done in reality, and although I haven’t tried it myself, it is reported that people quickly adjust to this reflected field, and somehow the brain “realizes” the correct orientation of the visual field.
But what does this say about the qualia of spatial orientation? It would seem that I myself would not be able to distinguish whether or not I am seeing a reflected field or the original field. This isomorphism problem seems to lie within the same mind, and not between minds. Both fields seem to map onto a “canonical” representation of spatial orientation that represents all isomorphisms of the same field.