It is the natural reaction of someone with her temperament, and someone who has been away from home for such a long period of time. She is being thrown from order into chaos- and it it never an easy transition.

However, I don't agree with you that Jane Austen is not aware of it. The phrases that the narrator uses makes it clear that Fanny is indeed exaggerating the advantages of Mansfield in her mind. And if her mother had shown some degree of affection towards herself, much of this would have been more bearable and overlooked.

She might scruple to make use of the words, but she must and did feel that her mother was a partial, ill–judging parent, a dawdle, a slattern, who neither taught nor restrained her children, whose house was the scene of mismanagement and discomfort from beginning to end, and who had no talent, no conversation, no affection towards herself; no curiosity to know her better, no desire of her friendship, and no inclination for her company that could lessen her sense of such feelings. Chap. 39