Graphic warning.
The probable cause statement just mentions the semen on the underwear but not from or inside her body. I would bet that the autopsy report documents whether there was semen inside her. Since she was found in the mud, that would be the only other way to find his dna, by looking inside.
Not sure what you mean by two pairs of underwear. They found hers and her shorts in the wooded area. They found his underwear in his room.
Why put the clothes back on?
I posted a couple days ago that I think the rape happened in a car. I think that she put the underwear and shorts back on because he said they would go home. Maybe he meant it. But then the blood got on them that way. She was probably crying and freaking out and he realized that there would be no way in heck that she could keep this a secret, he became enraged and decided he must kill her. Or he just started hitting her in rage to shut her up and just did not stop, and felt he had to kill her at that point.
In some odd way, was killing her a merciful thing after what she had been through with the rape, in his mind?? I never considered that until typing just now. Did he want her suffering to just stop? Did he know how horrible the rape was and did not want her to live?
Just speculating.