I'm just guessing here , but my take is that boughten oir custom bags were more likely to be lined  .  For me , the lineing is just a prroblem  , sooner or later you'll catch a hole in the lining and it'll keep getting in the way , Lining the flap as mentioned can have a practical purpose . The lining in the bag also would tend to take much longer to dry out if caught in heavy rain or a  dunking in crossing  water .  I know lining can make a pretty bag  , but for real field use I like mine without it .