In the sim theory, the external neural net tells us our brain is made of atoms.. you could theoretically feed your senses a Minecraft reality and you'd think your head is full of interacting blocks - which is still capable of performing the same NN functions as a wet brain... So I don't know, the brain could be made out of anything that fits the requirements of running the computation.
That's assuming there even really is one - senses can be hijacked, just like in dreams, so we may only think we have a brain - so strange.
Why then program the brain to try to understand that it's in a simulation when the goal was to create a realistic simulation in the first place? That'd be a rookie mistake on part of the simulation developers.
The neural net itself is built on a much simpler substrate in an external universe.