Well, this is getting interesting now. I'm going to have to connect up some test gear and monitor my hatch. I've never torn into the ECU with regard to it's potential role in controlling the alternator. I was always under the impression that it monitored only, and the voltage regulation circuitry was with the confines of the alternator - i.e. it operated a a Stand-Alone component.
What I do know is a little about lead acid batteries. Having ran RC models for many years and then racing go-karts with battery powered electronic ignition it's caused a little research on batteries, charging, maintenance, properties, etc.
For lead acid, a very general rule of thumb is the voltage is a good indicator of charge condition. Take a battery that's been sitting 12 or more hours off a charger or alternator and measure the output. 12.5v = ~50% charge condition. Each tenth of a volt over 12.0 volts can convert to a percentage of charge condition. 12.75v is ~75% charge condition, etc.
So, a battery would not be maintained in a properly working electrical system at 12.5v, it takes >12.6v to charge. (Evidently Honda does not consider this to be a problem)
Took a quick look at the link you provided - very interesting material. Educational to me for sure. I'll look at it more in depth tonight for my own education.
Thanks for sharing it.