Joush, I think you need some perspective in this.
Before the microprocessor was discovered, computers as small as modern iPads were impossible. Not unfeasible; actually impossible. To produce the necessary components for one to exist at the size modern micro-electronics work would have required violating the laws of physics. And then someone discovered the wonderful properties of turning silicon into chips and the modern computer was born. Even micro-electronics of the size used today would have violated the laws of physics. So, right now, you are using a computer that, 60 years ago, would have been utterly implausible.
Plus, you are forgetting to factor magic into this. You speak of internal logic and consistency, yet are leaving out the biggest and most important item: The Matrix came after Magic came back. Take a look at how it is that all of the tech which really, really closely interacts with the human neural system, including the Matrix, came after Magic returned. Stop and think about that and how it might have changed the way the technology was developed, as opposed to our own development of tech. Then it'll make sense.
Really you are just restating the idea that this can be ignored in favor of magical thinking vaguely justified by the setting, something that might work better if this was the first rather then fifth edition of the game.
As to microprocessors, they represent an important development but are not at all a point that people understood the possible implications of transistors. In fact, Moore's Law predates the microprocessor by half a decade and none would have said it was impossible to reach modern densities of processing power, though many would have considered it remarkably unlikely. The physics and properties of silicone semiconductors was well understood before microprocessors were developed and never would have violated the laws of physics, only defied contemporary understanding, an important distinction. If a law of physics is broken it is, obviously, not a law.
I will admit that producing an iPad in 1971 would be impossible, but the idea of a handheld computer was effectively understood and hardware and software designs did include clever and important systems to prevent the accidental (or intentional) execution of code that could be destructive. In fact, checking to make sure that code would not physically damage a computer was important in the long ago and far away of the 1970s. These days, such systems are integrated into the very design of the hardware.
This is a Solved Problem. Smallpox isn't rampaging though Seattle in Shadowrun, buildings can be cooled by heat pumps and optical material can be carefully shaped to bend light and allow those hard of vision to see clearly. These are assumptions we can make because if the technology to perform these task was lost the book really, really should mention it.
If remote commands with no permissions can damage electronics then it says that the machines are much worse then modern equivalents, not better. Within the setting it makes it clear that the equipment is worse then things available 10 years before.