There was no reason for CW to be barefoot at the house, not at the time he would be using a bag. He would be fully dressed and ready to leave. From the true crime books, articles, etc., that I have read, killers are so busy being smart that sometimes, they end up being dumb. (Sorry for this description) I think CW had a problem getting, at least one of the girls, through the hatch. He couldn't bare to look at them, so he covers them with the bag they had been transported in and uses his foot to push down (legs are stronger than arms and there's more leverage), But being smart he doesn't want a shoe print, so he removes his shoe, leaving a foot print. When he's done he throws the bag down, over the side and then forgets about it while he's burying SW. Since there seems to be no blood traces anywhere, perhaps he was very careful of not causing blood. In that case maybe the bag over the body, while it was in the hatch, was a barrier to blood and the shoe was removed because shoe soles do retain traces of blood, DNA, etc., in the nooks and crannies. Feet can be wiped off or washed. The DA did want prints and measurements of his feet. IIRC. Again, sorry for the descriptions. Any way you turn, it's horrible.