You seem to be presuming the upload would consist of taking the input-output map and, like a smart compiler, trying to invent the least amount of code that would produce that, or in another metaphor, try to optimally compress that input-output map. I don't think this is at all how an upload would work.

Well, presumably you don't want an atom-by-atom simulation. You want to at least compress each neuron to an approximate input-output map for that neuron, observed from practice, and then use that. Also you might want to take some implementation shortcuts to make the thing run faster. You seem to think that all these changes are obviously harmless. I also lean toward that, but not as strongly as you, because I don't know where to draw the line between harmless and harmful optimizations.