Lots of things impact a person’s overall spiritual state. What determines how ‘good’ or ‘bad’ you are is entirely in the realm of bechirah, but the spiritual levels that one attains and/or is born into depend on a lot of other factors – kavanah b’shaaz tashmish, yichus, upbringing, and many others. A kid who is a ben niddah and a mamzer that grows up in a drug home is not born a rasha, and can become a big tzadik by making the right choices, but he is spiritually impaired and has a defect because of his circumstances.
It’s kind of like the difference between a malaach and a person. A malaach is objectively on a highway spiritual plane than a person, but a person is greater because of their ability to reject evil and choose good. So too, a baal yichus is greater in their objective spiritual level, but if they don’t shteig, they are not as good of a person or as important to Hashem as a person born to disadvantageous circumstances who rises above those inhibitions to follow Hashem and His Torah.