Even still, the isolator/secondary battery solution would not solve the M3 'hard off' dilemma. The advantage of going the PicoUPS-120 route is that the M3 is never connected directly to a permanent 12v source, therefore I will never run the risk of the M3 discharging my car battery while the ignition is off. Instead, the PicoUPS charges off of the ignition line and supplies 12v 'battery' voltage to the M3 on the PicoUPS output.
I did do some tinkering over the weekend and with a makeshift serial cable, I was able to connect the M3 to the external RS-232 line of my CarPC - using the downloadable software from the Mini-Box site. It appears that they have limits on their 'custom' settings, with the upper-most threshold on the 'hard off' delay being a time of 17:59:59. I believe this limit to be the result of the system code using a 16-bit integer value on the variable used for number of seconds - i.e. 17:59:59 equals 64,799 seconds, just shy of the 65,535 limit of a 16-bit integer.
I'm awaiting a response from the folks over at Mini-Box, but this limit will suffice for daily use (provided the small lead-acid battery will last this long), and much better than the two-hour default settings. The only time I will need to perform a cold boot is if the car is not used over the weekend.