Otaku have been either created by the Deep Resonance or by an AI. So it would be conceivable that nuanced biofeedback can change the brain to create the Otaku abilities. With technomancers and certainly technocritters this becomes more difficult, but it's still possible to think that it's some naturally occurring isolated genetic trait to receive and manipulate matrix signals and the rest is learning to use it. (The case for a genetic component is made in Augmentation p. 78-79, twin studies and all.) It would probably be a biological system that has some functionality in all individuals of a species but only in techno*-individuals is a variant present that enables interaction with the matrix. Other animal species just happen to have the same trait, probably most of those animals affected that are also exposed to matrix signals can't actually cope with it, but then you have the odd specimen with higher than normal intelligence and you get these animal hackers. It's certainly a stretch but also not inconceivable assuming some artistic licence, which is necessary to make the whole concept work in the first place.
Now, if technomancy was an adaptive trait, we would need some kind of component-level genetic change and a semi-directed one, because it's a complex trait (receiving and manipulating matrix signals) that has pretty much sprung up at the same time and even across species boundaries in response to a new phenomenon. Here a mana-induced genetic change would actually present itself as a likely solution. And since technomancy and magical ability are mutually exclusive, I could certainly think of the former as some kind of awakened trait that failed to properly express especially if it was the signals of the technosphere that somehow disturbed it's development. Now that is not to say, that technomancy is itself a magical ability. I would find it difficult to actually introduce such an explanation at this point. Because if technomancers were manipulating mana, we should have heard about that by now. Many of them will have been closely assensed while using their abilities.
But in the end we are probably dealing with the shifting vision of how technomancy (and otaku abilities before that) works. So the tidbits we are presented could actually refer to different explanations and I would not expect them to all work together. Just one more example, System Failure describes the case of Alexandra Paris who obviously exhibits technomancer abilities pretty early on, 2065 or something, and she was connected to the matrix during the Crash 2.0 as with other cases of AIPS. So, I think the early explanation for the occurrence of technomancers was that they were exposed to biofeedback from the crashed matrix, so we are back to Otaku-like brain rewiring. Emergence basically says so. But how then do children who never experienced the crash and never get a DNI develop these abilities? The germline of their parents was also "rewired"? No, I think at that point they just went with well it's a convergent phenomenon: evolution, adaption, something, so maybe it's not even a singular explanation behind every case of technomancy.