There's a joke in electronic engineering about transistors being invented to protect fuses. Basically, it means that transistors blow faster, and so a fuse is practically worthless for that purpose. It still protects the wiring from catching fire, but not the circuit from functional damage.
To protect the circuit from functional damage, the designers therefore have to ignore the fuse and design the circuit itself to take whatever abuse that might be. That requires more parts and complexity that adds nothing to the functionality (and occasionally interferes with it), and so the less-likely scenarios from a normal-use perspective are often omitted, leaving the circuit vulnerable to them.
So basically anything beyond letting the car as an entire system do what it's supposed to all by itself carries a risk of damage if you do it wrong. Sometimes you're forced to interfere with it, like if you have a dead battery and need to charge it externally, but it still carries that risk and so you need to be careful about it.
I suspect what happened in your case is that when you hooked up a dead or very weak battery to a good one, backwards as you said, the good battery "won" and forced the bad battery to a negative voltage. Pretty much every silicon chip appears to be a short circuit past about 1.4V applied backwards, and so you got a bunch of current flowing backwards through a path that was never designed to do that.
If you're lucky, then the first device to start conducting effectively limited the reverse voltage to its own threshold, and everything else could still (barely) handle that. If you're unlucky (and more likely the case), then there were a bunch of devices that reached that point, and the relative current through each one depended on the relative wiring resistance that fed them. So now every electronic device in your car has that on its record as a possible latent failure mode.