] Though better endowed than the elder sister, Mary had not Anne's understanding or temper.

Because "endowed" is followed by a description of Anne's intelligence, the endowments, or gifts, of her mind or talents, if you will, I believe it refers to Mary's personality. My dictionary has a secondary definition of "endow" that reads: "To equip or supply with a talent or quality: Nature endowed you with a beautiful singing voice." So Mary's personality, or temprament, is better than Elizabeth's, but not as good as Anne's. ;-)

] In person, she was inferior to both sisters, and had, even in her bloom, only reached the dignity of being "a fine girl."

I take this to mean that she - her physical person - was not as good looking as either Elizabeth or Anne (before she lost her bloom, of course). Remember that earlier Mary was described as "coarse."