I'm still wondering how the OP is measuring 6 gallons of hot water vs 4 gallons. After about 4 gallons, the output temp HAS to be reduced since you are replenishing the tank with unheated water. Regardless of how the intake tube and output tube is setup, it would still mix somewhat. So it would seem to be impossible to get 6 gallons of hot water out of a 6 gallon water heater UNLESS you drain it from the bottom and do not add any additional water to refill. Or am I missing something blatantly obvious (wouldn't be the first time, but...)?
