Always enjoy reading threads about battery and charging methods/systems, there are so many differing opinions.
In a former life I was an eng for HP. Had one assignment investigating different battery chemistry's. One of the battery types was LA batteries. Think that puts me in a place where I know a little about them and associated charging systems.
Not familiar with all the Yanmar electrical systems but do know a little about the one on my tractor. The alt is fairly small, about 15A max. Power out from the alt is A.C. and is rectified by the VR. The alt uses a permanent magnet and not a electromagnet field winding. This design is not unlike that found on most small engines like B&S, Kohler, etc. The only way for controlling voltage is to shunt power in excess of that needed to charge the battery and run lights, gages, etc. The alt is always putting out max power.
Now, for a nom 12V LA battery that is fully charged and has been at rest for several hrs the nom voltage should be close to 12.7V. Typ charge voltage via a alt/generator is ~ 14.25V. LA batteries typ have a fairly small self discharge rate, ~1%/mo of remaining capacity.
You really need to take some voltage readings. Battery with engine not running. With the engine running take readings at the alt output (remember output is A.C.) and at VR output and at battery terminals. I would expect to see a reading at the alt >14V. Should see voltage at VR output and battery the same voltage. Due to the small capacity of the alt, the voltage at the battery will vary depending upon how much of a load is being placed on the alt for charging and running any of the electrical acc. With lights off one should see a voltage higher than it was at rest and slowly increasing until it bumps up against the VR setting which should be about 14.25.
I could envision a VR design where when there is no battery attached, all the alt power being shunted to ground so there isn't any power available for the lights, etc. Could be all wet here but think this is a possibility.
