Kenny,
Actually, it's also for (perhaps more so) a section of the servo amp circuitry that wants a stable voltage. As the instructions tell you, using a common battery for the receiver and servo reference (while using another battery to run the servo motors) is "acceptable". Reason is because they both draw very low current (relative to the servo motors) therefore allowing the battery's voltage to have no noticeable instantaneous drop. That also explains why Citizen-Ship says you can use a lower capacity battery for these (the Rx & servo ref). A servo motor under a heavy load will draw a relatively high current and will bring the battery's voltage down, at least while the load is present and especially if the battery's charge state is on the low end. Remember we're talking about relatively small batteries here - not your 12 volt car battery that has tons of amp-hours. Also remember that when the Citizen-Ship analog radio was introduced, ni-cad battery cells were were still a relatively new item and not the higher capacity, more reliable cells used by RC'ers today.
Anyway, that's my theory / explanation and perhaps someone may want to elaborate and explain why the old servo needs the reference voltage. But don't let any of this scare you away from using a common battery pack to test out you radio. Even if the pack is run down while operating the radio, it won't harm the circuitry. Might not be good for your airplane if your flying it, however! I've used the one pack method to test both my 3 and 5 channel Citizen-Ship analogs.
Tom