jrc, mostly likely there's a clue to your question everytime you start your car.
Turn on ignition and radio but don't start car. Now start the car. Did radio stay on? Hmm, wonder why that would be
For the starting application the system voltage is uniform. For damage to occur on devices you need the
relative voltages to be different.
Draw a fish diagram of a car battery system and everything hooked up to it. Now draw in a 9V "capacitor" to the system through a switch which is basically what the memory hold device is when you plug it in. Close the switch and tell me what the current and voltage transient would be.
Car techs can scoff but there is numerous reasons manufacturers state in the manual to disconnect the battery prior to working on the electrical system.
When we work on parts on the bench during development, it's very common for us to misconfigure the bench set-up such as turning power supply knob wrong way, forgetting to set current/voltage clamps, and other stupid things we do (we're human). It's not uncommon for a part your working on that was reading perfectly to "change" when you do make a set-up mistake. Part may still function but now it's out of datasheet spec or a host of other weird peformance issues. Bad design? Maybe, maybe not, but once you take a part and hit it with something it was not designed for all bets are off. Some of the changes are subtle.
Me, I would not touch my car with a 9V memory hold device. Best place to store it would be the garbage IMO. The reason you don't see widespread issues with people using the memory holds is largely due to the protection schemes inherent to the design.
If we really want to deep dive, "9V" batteries are 9V or all the way down into the 7V range versus a lead acid battery which is 12.5V+ with alternator not spinning. Thus, voltage differential in real world is higher than 3V....
The parasitic transistors on many parts in automotice system are referred to as the body diode. It's related to the dV/dt, not just steady state conditions (although they do apply). You decide if not having to reset your radio presets is worth the chance of doing something to your car.
Many manufacturers are now putting non-volatile memory on electronics. Way more details than I want to go into but you'll have to hash that out with the product and applications engineers if they should add it or not. Memory to hold ECM/PCM stuff is important. Radio presets, not so much. Cars get expensive $0.50 at a time so be careful about those seemingly trivial costs.
PS: No such animal as a transistor battery.