Just like they know their auto’s where some manufacturers consider them sealed for life
put it this way, when you rebuild an engine do you torque the head bolts up to what old mate says at the pub or the manufacturers specification?
again we can all sit here and speculate like old mate at the pub or you can follow the specifications from the people who designed it.
I recall being asked to look at some expensive modules (~$5000) that kept failing in some heavy vehicles. I had a nice little sideline fixing (hundreds of!) these modules for a while. It was a design fault as these modules just weren’t designed to tolerate automotive voltages. I enquired as to what they (the vehicle manufacturer) actually specified to the manufacturer of the module. It turned out that this major US manufacture hadn’t explicitly or correctly specified that the module had to be spike tolerant. I ended up designing an add on module to filter out the spikes. These add-on modules then became an official required fitment in the service program. So I do really understand what‘s involved. And, I have firsthand experience of a major vehicle manufacturer stuffing up the supply specifications on a module.
So, when having a flat battery, I would firstly (bench) recharge that battery. If bench recharging wasn’t practical I’d do the jump start procedure but not disconnect while the cars are running. It’s small difference (to what the manual states) but one I’d personally do. Why do it the other way and (albeit remotely) risk an electronics failure.
you cannot broadly assign one experience from one set of vehicles to every vehicle, if the manufactures guidelines call for a certain procedure then there is a reason for it.
again it is no different to any other service procedure, there is a reason these things are formulated and they vary with different vehicles which is why they take the time to provide the correct steps necessary to complete the task.
you can apply what ever theory you want to something like a jumpstart procedure but that does not mean it is the correct way to do it.
it is no different to any other service guideline from using correct torque settings to transmission servicing steps to jumpstarting, if the manual states to do it a certain way then you do it that way.
edit: over the years i have read some of the steps provided by manufacturers for all sorts of things from computers, to plasma machines, hydraulic presses to automotive applications and many times i have not agreed with the steps but i still do it that way because there has to be a reason for the steps and i know i did not design the machine so i just do it the recommended way whether i agree with it or not.