It kinda seems like we could direct the AI to build a huge number of research nodes and to study exhaustively these effects, seeking a safe electrode or nanotechnology wiring that tricks the brain into thinking that it's friendly. Or a mixture of drugs that does this. Or enough rules for life support that someone's immune system can be safely shut down. Or...

Basically there seem like there are a lot of ways to accomplish this once you can start manipulating biology with more consistent results, and you can practice on millions of samples of human brains (nothing unethical, just small batches of living cells from living or deceased donors) and learn from them all in parallel.

I mean no human scientist alive can learn from a million experiments in parallel so of course we couldn't figure it out. It's too complicated, there are obviously thousands of variables.

And there are an awful lot of ways to succeed is my point. Genetically modified neurons that get introduced, they synapse to our cortical columns, and then they grow into new signaling molecules never used in humans before, borrowed from another animal, that get emitted by the electrode grids which are embedded in sheets surgically installed. That might solve all problems you mentioned above because these modified 'bridge cells' can have the behaviors programmed in to not become inflamed and to synapse well to artificial electrodes.