IMO it's not even the case of Bonnie not having the rights to those songs, it's just she either grew out of them or she's saving for the album. She's a songwriter and she definitely wouldn't let someone have the rights to her songs, because even if she didn't want them for herself, that would stop her from selling them to someone or something else.
Also, looks like she really left Kemosabe, the label on iTunes is just Bonnie Mcke Music