Silly, Silly, Silly! I agree, it's not only a useless feature, it's a conspiracy of errors.
If you put anything heavy in the cargo pockets of your baggy shorts, or move about (as you do when riding technical terrain) the baggy shorts will pull down or move around your waist, then, being integrated, they'll pull the waistband of the liner short down too.
When the waistband of the liner short moves down the chamois will no longer be held in intimate contact with your crotch. The chamois' primary function is to eliminate chaffing, it's works in the same way as moleskin can to protect your feet from blisters, like a prosthetic callous. The padding itself is almost a secondary feature, though more padding is normally be better IF it's in intimate contact with your butt. However, if your liner shorts are pulled down by your baggy shorts, a thick pad that's not held in intimate contact with your butt will feel like a full diaper, which is particularly unpleasant when it's sodden with sweat and you're off the bike hiking.
A waistband can only cinch around you, so once things move South it won't do anything to bring the chamois back into place; the only fix is to hoik them up manually, at which moment movement and elastic fabrics will instantly begin conspiring to pull everything down again. This is why distance cyclists wear bibs (roadies don't even have heavy, cargo laden baggy shorts to contend with). Bib straps pull UP from the shoulders, keeping the chamois in prosthetic-chamois-mode. Not having a tight waistband (which is a little uncomfortable and can restrict your diaphragm breathing) when you're hunched over the handlebars is a side benefit.
*Yes, I'm the DirtBaggies guy. So you could argue that this is just my pitch. Well it is, I believed my pitch so strongly that I started a company and made stuff to try to rectify this.