This is my opinion only. There are several reasons I may choose to go with an "added" flap versus one piece of leather:
1) Yes, a one piece folded bag takes a bigger piece of leather, but this is not my primary aim.
2) I sometimes like to use a thicker piece of leather for the flap so I can scribe a design in it. A thicker piece of leather would make an unyielding hinge.
3) I like to line the flap so that it has more body, is more finished looking, and/or has more weight to hold itself down with no fastener. I can also hide a piece of flattened lead in the bottom of the flap to keep it down.
4) The line of stitching from the hinge to the flap give more body to the top of the flap and holds it straighter.
5) The line of stitching for the flap to hinge gives a subtle bit of decoration there, and the bottom edge of the hinge can be pinked or scalloped to give decoration.
6) A big reason is that I make my bag body and stitch it up first, then judge how wide I want my flap and how long. It is one of the last elements I do. Especially with inside-out bags, as they all turn slightly different and end up different widths. I leave the hinge a little long for the same reason, and trim it back to suit.
I hope this explains my thinking a little. God Bless, Marc