You don't necessarily need to understand something to a deep degree in order to simulate it. Ptolemy created a very accurate simulation of the solar system with a wildly poor understanding of how things moved, just because the system was simple and very consistent.
Simulating a fly is obviously a much larger task, but "we can't possibly simulate it unless we understand X" seems to me a misguided criticism.
Sure, hopefully there are many details which we could ignore, like we can ignore what the planets are made of. But from what we know about how nature works, I suspect a lot of little details are going to matter.
Flies are pretty highly optimised, and nature is happy to optimise all the way down to the single-molecule level. In fact there has to be a good reason to do something at the whole-neuron level, as this is vastly more expensive than doing it with a molecular machine. That reason is often speed, as electrical impulses give fast long-distance communication. But if you can do some of the computation with a molecular machine before sending that fast signal, why wouldn't you do this? So I'd bet that the hardware is customised many different ways invisible to this kind of scanning.
It seems to me that fundamentally people assume that simulating a neuron is vastly, vastly simpler than simulating a bacterium. Ok, you can assume that. But what gives you confidence in that? Do you think that simulating a bacterium is less complex than simulating a fly, or about the same?
It all depends on what questions you want to answer with your simulation. If what you care about is where in the room the thing will be after 10 seconds at a resolution of 1 cubic centimeter, then yes, simulating a bacterium is vastly simpler.
In principle I agree with you, but unfortunately we already know from other research that specific neuro-transmitters have specific effects on observable thought processes. Some neurons also sometimes 'broadcast' neuro transmitters by releasing them in an area around them, not just through direct synapses.
To me it would be highly surprising if these effects were not absolutely necessary to the brain's working.
Simulating a fly is obviously a much larger task, but "we can't possibly simulate it unless we understand X" seems to me a misguided criticism.