Jacobs seems to know herself that something is up with her ending:
Reader, my story ends with freedom; not in the usual way, with marriage. (41.25)
By “the usual way,” Jacobs means that both novels such as Jane Eyre and slave narratives like Narrative of the Life of Frederick Douglass, an American Slave typically end with marriage and a retreat into comfortable domesticity. (We didn’t pick Jane Eyre out of a hat: the last chapter of that book begins with the sentence, "Reader, I married him" [38.1]. Sounds to us like Jacobs is making herself a little allusion, there.)
So, Jacobs is saying that she knows perfectly well her ending is a little off. Although Linda is free now, she still lives in servitude to Mrs. Bruce and her life’s dream—“to sit with my children in a home of my own” (41.25)—hasn't come true.
And it's not just that this traditional marriage ending hasn't happened. It seems like Jacobs might not even want that tradition ending. See, white women of your typical nineteenth-century novel and the African-American men of slave narratives seem to value marriage as the ultimate goal of life (and of their stories). But not Linda. Linda values legal and physical freedom.
When you think about it, this makes sense. For women in the nineteenth century, especially the first half, marriage meant that you basically became your husband's property. Now, we're not at all saying that it was like being a slave—but it was definitely a kind of legal bondage. So why would Linda want to end by becoming someone's property again?