I'm Japanese but it's incomprehensible little bit to me too.
髑髏 (しゃれこうべ) is not usual word in these days and sounds little bit strange (goofy, should I say?). We use 頭蓋骨（ずがいこつ）to mean "skull".
It's just a joke without any reason. but somehow it's funny in certain situation, like tense situation or lifted up at midnight on trip. Because, there's no reason.