Because like a car boot, unless you leave loads of empty space, the thing you want is always at the far end and needs you to move other things to get at it.Longflaps or trunk bags are better because they open along a long edge and so stuff can't be buried so deep.
I use one of these to put my clothes in, pack it off the bike, then slide it in like a parcel. Simple.
https://www.amazon.co.uk/eBags-Packing-Cubes-3pc-Set/dp/B004YLIS9Q