Your first paragraph is an exact illustration of what happens when you start the Yanmar with fully charged house batteries - even if you have, as we do, a 3-stage regulator on the Leece Neville alternator. However, I omitted to mention that we also have a field disconnect switch for the LN alternator so that if the house bank is fully charged and we want to motor, we can disconnect the field wire in the alternator so that its output is zero.
Another issue with rewiring the LN alternator with a 3-stage regulator is that if your batteries are down and you start the Yanmar, the LN will put out maximum current (175Amps) until the battery voltage reaches 28.8V. The LN alternator is not "hot-rated" to produce maximum current continuously. If it is putting out 175A continuously eventually it will burnt itself out - you'll smell it before it dies !
Two solutions to that - easy, immediate, start the genset and turn on your 100A charger until the charging current gets down to something manageable for the alternator...say 130A.
More complex, put a high wattage rheostat in the field wire from the regulator to the alternator so you can reduce the field current and thus reduce the LN output to safe levels...I have this all set to go, but haven't yet installed it.
Your second paragraph illustrates a potential, but unlikely problem. Automotive alternators such as those used on the Yanmar and Onan are very reliable as long as they are looked after. If you disconnect the battery from the alternator while it is putting out you have the possibility to fry the diodes in the alternator. The only real solution to your scenario would be to have a "kill" switch or field disconnect switch in these alternators also.
I don't have this given that I believe the risk of your scenario is very low.