[Al Skierkiewicz]

Sorry I didn't weigh in on this earlier...
The original PD and cRio voltage dropout was lifted from automotive industry papers on electrical devices on vehicles. (One of those is a Daimler/Chrysler paper) In those recommendations, devices should be reliable down to 6 volts and are classed by importance based on the functionality of the device. (used only during cranking, used only during engine run, etc.)
The original control system wanted to be better than that knowing that FRC is a very harsh environment. The power supplies on the side car dropped out at around 5.5 volts. When that level was reached (if the input drop was long enough that the capacitors on the side car finally dropped below 5.5 volts) the sidecar would cease providing PWM output. In terms of a fully charged battery and ideal conditions, a robot load current of about 600 amps would drop enough voltage across the internal resistance of the battery to achieve that. (That is in keeping with the manufacturer's maximum current spec for our batteries.) If we add to the equation, the real world voltage drops across wiring, main breaker and typical wiring, that level can be achieved with a load current of approx. 500 amps (or less depending on robot design). The power supply for the PD ceased functioning at approx. 4.5 volts. It is pretty easy to see that the big CIM motors at 131 amps stall could easily approach the dropout specs with only a four motor drive. (In reality, with good wiring technique, a CIM motor in stall, driven by a motor controller, can draw between 116 and 120 amps.) It appears that the RoboRio spec and brownout behavior are consistent with those electrical considerations. Remember that long wire runs, poor crimp and termination techniques will degrade the available voltage at the RoboRio and other systems.
As to the backup battery on the old IFI controller, that was a design choice made by IFI to overcome the brownout conditions at the time. Remember that the controller was an old technology (compared to today) and would take a while to boot up and start running code. To keep the controller up and running, a circuit that switched the CPU (and attached circuitry) to battery supply during brownouts was a good choice.