Talking to the wrong ICE can cause brain damage too, so brainchips needn't require anything more invasive than whatever normally happens over the network.
Oh yeah, this is super speculative. And I agree about Fetal and Mutate, I think most of the work is being done by Braintrust, Genetic Resequencing, and now, Allele Expression.
I got to that conclusion in two steps. First, Braintrust. If some of your computing (and therefore perhaps some of the contents of your HQ) is done by disembodied brains, then triggering certain memories can be a matter of regulating the expression of certain genes in those brains. That part's easy, and we could call it a day if it weren't for that darn rat.
And that was when I started thinking about Genetic Resequencing. Resequencing doesn't just get you more mileage out of your Nisei clones, it also makes House of Knives better, it makes Executive Retreat better, heck, Mark Yale can even monetize a "resequenced" Utopia Fragment. That (and the mysterious Allele Repression) provided the basis for my speculation that Jinteki uses more wet- and bio-ware than even Braintrust let on.
None of which addresses your main question: what is the allele of interest doing in a rat (and not even necessarily a lab rat, but one that appears to be in a sewer)? My best guess is that storage is expensive, as is maintaining a population of research animals, but sneaking down to the sewers is free. It's still a ridiculous reach, I know. I guess my only defense is "why else a rat?"
I think the ice may have been designed around that particular metaphor because of the way NBN often processes tags and marketing data. It's very indirect and probabilistic. Pachinko doesn't just identify you and strike, like Universal Connectivity Fee, it runs you and the rest of the network's traffic through this statistical maze, subtly rigged so that any undesirable "balls" will eventually be sorted out of the server.
...I'm reaching here too