Same with the solar system. We can create simulated solar systems. We will probably be able to make simulated brains. What is your point?
Alright, assuming the first AI even is a simulated brain (I don't see why we can't invent intelligence from first principles first.) We could definitely tweak it. We know of drugs like amphetamines that enhance human ability. That's like Stone Age tech compared to what's possible if we had unlimited control over every neuron in the entire brain. Not to mention just adding more neurons and making a larger brain. This is just touching on what's possible, I could go on for ages on possible improvements.
In everyday life, we treat other minds more like "maps" than like "nuclear reactions". We interact with nuclear reactions by getting radiation sickness and dying. We interact with people through more indirect channels. A simulation could be at the other end of the channel and we wouldn't know. Maybe he wouldn't now, either!
We don't get electrocuted when our interlocutor's neurons are firing, the effects on us are only through his external behaviour. It's the abstract informational flow what seems to matter.
That sounds like a really interesting experiment. Have you published your data?