That would be correct. The issue is you have 2 batteries tied together via huge cables that can handle a load. If you hook a 24 volt trickle charger to the system, it will charge both batteries without disconnecting anything at all. The point the mechanic is making is that if you disconnected the massive cables and allowed each battery to be charged separately, it would make for a better charge since the state of each battery is considered separately. You can't do this with them connected as the charger looks at both batteries as 1 big battery.
However, if you consider the fact that when you're flying the airplane your airplane is doing exactly this and charging both batteries together as 1 big battery, then I'd argue that the difference it would make by going to all the trouble to separate them really is overkill and not worth the effort.
Also, you would NEVER use 2 chargers together when the batteries are still wired together.
That's my 2 cents :-)
Glenn