I believe it's still Mio. as you said she looks like Mio but also if we look at the cover artwork for the album
Source: K-On Wiki
we see the other girl is Mio's shadow suggesting some connection to Mio while Mio's Gallery lists her as her "doppelgänger"
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.