I just bought a new sailboat with flooded batteries and Balmar charger. The program for these batteries starts at 14.6 volts, which is above the 14.4 that you mentioned in the PY article. The engine battery is up to 14.8 volts when charging off the engine, as the batteries are isolated. Should I change to a different program to avoid this? The boat is new to me and I believe that there is a temperature probe. I am not sure if the probe is on the house batteries or the engine starting battery, which is the one being overcharged when we have been at anchor and the house batteries are depleted to 12.2 volts or so. The engine battery is still at 13.2 volts, so I assume that the Balmar might be overcharging the engine battery as it is producing full voltage for the house batteries.
If your regulator is battery temperature compensated, please remove the temp probe and calibrate your regulator so the batteries gets charge at no more than 14.4V. Once calibrated, re-install the temperature probe and the voltage will be adjusted to the temperature of your batteries. The alternator output should be primarily connected to the house batteries since they are the batteries that need a charge the most. The engine batteries might get slowly overcharged (if in parallel with the house) while the house gets the right charge. This charging arrangement is quite common and a good compromise. Make sure the house do NOT get overcharged.