BOTNTools? Back when I used it to edit a couple of girls I only edited traits and those did reflect in the game properly (giving a character with small breasts Buxom 3 made her have huge tits the next time I played).
There is a section where you can edit all the typical slider stuff (eye distance, butt width etc) you saw in character creation, but they have the same, very specific numerical value system (i.e "LipLowerWidth: -0.448626") so I never actually edited any of that but it does let you. Traits are simply either check boxes or a drop down where you select a level.
You select a girl from a name drop down menu to do all this, I don't know if you can edit the stuff randomized nephs in the wild spawn with. Kind of want to check now to see if I can make every bovine girl in the wild spawn with the Massive height trait