It's all in the voltage, not current.
A battery cannot be overcharged unless there is too much voltage going into it (greater than 14.5V typically, though some batteries can tolerate up to 14.8V). Without voltage, the battery doesn't accept current.
Basically, when one battery approaches full-charge, it's terminal voltage will rise until it matches with that of the alternator's regulated set-point voltage, and current will then taper off to that battery. Meanwhile if the other battery still is less-than-fully-charged, it will have a lower terminal voltage and will continue to draw current from the alternator (current flows from a higher voltage to a lower voltage). As the 2nd battery finally comes up to the alt's set point voltage, the current to it then tapers off as well, leaving both batteries at or near full-charge.
For a regulator to see past a diode, it needs to have an external sense wire. Having this, it simply monitors the voltage right at the battery itself. If it's less than ~14.5V (it's set-point), the regulator sees this and steps up the current (up to the alt's max ability) until the voltage reaches 14.5V. Once at 14.5V the alt simply holds it there, effecting absorptive charging of the batteries.
Where the topic of the Scangauge page comes into play is when the voltage drop across a diode affects an externally-sensed alternator's voltage regulating algorithm... If the battery that is sensed by the regulator is taking heavy current, the diode's v-drop causes a corresponding rise in the alt's output voltage (the alt ramps up it's output in order to maintain 14.5V at the battery). Ahead of a diode this voltage can be as high as 16V. Remember that both batteries (diodes) are connected to this same output... A lesser-discharged battery will draw less current, therefore the v-drop across it's diode will also be less. If this battery happens to be the one not sensed by the regulator, too much voltage will end up reaching that battery (overcharging it). If your alternator's regulator does not use an external sense wire, then there's no need to worry about this happening.
Hopefully that makes sense.