What you said. How do they know the skulls weren’t placed there as a warning? “This is what we did to your siblings for not marrying the right people, and we’ll do it to you if you don’t mind us!”
Maybe decorating with skulls was simply all the fashion in those days. The more skulls you have, the fancier your home.
Actually I'm only being partly facetious. People interpret the significance of a lot of ancient items based on no real knowledge of what they meant to the people at the time. For instance, I once read a discussion about the significance of the small statuettes of large-breasted women that are assumed to be fertility symbols. But in fact, we really don't know that's what they were, for all anyone knows they were ancient porn.