That sounds like a situation where his Grandma did it because over the long bake time, 6+ hours for Scratch Beans, the Covered Bean Pot loses moisture , now she added more water and cooked it Uncovered for 2-3 hours more, until the beans were tender and the sauce reduced to the desired thickness... She passed this recipe and method on to his Mom and Mom on to him...But...Somewhere along the line the real reason to add more water got lost and he thinks this gets a more concentrated flavor.
Think of it this way...If you dump a can of Coke in a pot and cook it down to 1Tbs of Syrup...Then add " 12oz of Water " and cook it down again to 1Tbs of Syrup...Do you get a Double Strength Syrup?
Now, take the pot and add a can of Coke. You cook that down to 1Tbs of syrup... Add " another can of Coke " and cook it down again until you have 1Tbs of syrup...Now you got double strength Cola Syrup.
I too grew up eating nothing but B & M Baked beans from a jar, doctored up with Bacon, Onion, Ketchup, Mustard and Brown Sugar. Mom added her ingredients and simmered to thicken and meld the flavors. Yes the beans were REALLY soft but tasted great.
My MIL, born and bred in Boston, had her mother's Bean Pot and only made beans from Dry Navy Beans soaked over night, simmered until the skins softened, she drained them and baked layered with Salt Pork, Onions, Mustard Powder, Molasses and fresh water to cover.
You have a choice...You can take the B & M Beans, as is, add what you wish and Smoke/Bake to the thickness you want, uncovered, on the Egg. They will be really soft but will be the thickness you want and have a more intense concentrated flavor.
If you want a quick cook, maintaining what texture the beans have and your flavors added...Strain off most of the liquid, add what you want and just Smoke until heated through and the flavors combined...JJ