I think this is a good point, but I would go one step further. Because there was more than one crime committed. In addition to a murder, somebody tried to stage a burglary. Common sense says that whoever staged the burglary was also involved in the murder but it's still 2 separate crimes.

It seems to me that the prior probability that the person who staged the burglary is someone closely associated with Kercher, such as a roommate, is actually pretty high. A close associate would have a strong incentive to try to make the police think that a stranger committed the crime. Whereas a stranger or remote acquaintance would have little or no incentive to do so.