I can only think that LH might have admitted to a relationship and prior activity with Kayleigh but denied killing her. But if there are signs of rape, then the charges relate to different incidents... LH's prior to death and SB's at the point of death.
The only way we can really find out is to wait for further information.
From this new information I would conjecture that Kayleigh willingly met up with LH but at some point was accosted by SB, presumably without LH's knowledge (or his charges ought to reflect his knowledge, which they don't).
SB's FB says "single - male - interested in females" in the relationship status space. That doesn't necessarily mean he was only interested in females, not everyone is out of the closet, but everything I see fits with the declared status.
His FB has been described by people here as being the more 'normal' of the two men .... but I didn't see a lot of personal stuff on there to make any judgement? It seemed to be mostly business stuff on both his personal and business pages? You can't assume everything is 'good' just because some things are kept more private ... at the same time, privacy doesn't mean someone is hiding something bad.