The bottom of the trunk does not have to be flat either, that's a personal preference.
Having the box at a certain depth will eventually having it show from the outside(Gen1's).
Angle the rear bottom of the box up higher to match the side of the gen1 tail, and you can still have a little more depth in the front. As opposed to having the rear the same heigth as the front(level bottom/floor of trunk), and losing potential storage.
The depth of the box only depends upon rider weight(and passengers, if any), so that the top of the tire doesn't rub the bottom of the trunk over hard bumps. Otherwise, it's looks from the outside and preference of size and shape inside.
The cut outs are much the same, you can do whatever you like with the box.
