I can speculate, though :)
You can periodically pulse the circuit at a low voltage and figure out the resistance, and if the voltage is low enough, you won't power anything up. When the ignition goes into the ON position, you've got a huge drop in resistance as fuel pump, and other necessary electronics get enabled. A sudden drop in resistance is a good signal that you should turn the power back on. This will not work with some more recent electronic systems, but should work great for most mechanical ones. Pretty sure you haven't solved things like the interaction with a BMW battery monitoring computer, for example, and those cars will probably reject your battery with some crazy error after a while.
It's good that you've got space for more reserve capacity, parasitic drag is getting higher as cars get more fancy. For example, radiator fans and turbo oil circulators can run for quite a while after the engine is off.
Your super capacitor design is elegant - you can charge the supercap off the battery slowly, even at low state of charge where its voltage would sag too low for the starter relay if you were directly using the battery.
I have a little car which I race and weight matters, so I've been using a ~12Ah LiFePO4 home-made battery for a while (A123 cells). This is a very durable little battery chemistry. No fancy super-caps, though, I just keep mine topped off and starting the car puts the battery cells close to their maximum discharge current.
I wish you guys the best of luck. Lead acids are pointless with modern battery technology.