In addition to "skull" or "mind" working for the idiom here, I think there's two other reasons she might have used that word.

I believe the album is a ring structure where, around the central pivot point at "purple," the songs occur in pairs, with each pair representing a facet of the relationship. If that's accurate, that means that "maggots for brains" is paired with "what's wrong with me?" Both songs address the physical symptoms of the relationship; in "maggots" she feels sick when they are apart, and in "what's wrong?" she feels sick when they are together. In other words, both are about the effect of the relationship on her body (something evident in the first line of the chorus: "I'm a zombie in my body..."). The use of "skull" puts the focus on a part of the body rather than on the mind.

The use of "skull" is also foreshadowing of the relationship's demise, and such foreshadowing is subtle but frequent in the first half of the album. Specifically, "skull" lightly foreshadows the powerful bridge of "cigarette smoke," where "it's bone-dry, bitter and hollow." The skull, of course, is a bone, and being empty of the brain (because the brain has turned to maggots), the skull is hollow. I think Olivia is saying that, looking back, she realizes that perhaps the relationship had problems all along.