The meaning of a clause

Dear Teachers,

I have a question as follows.
Thank you in advance for sharing your time and idea with me.

1) In the underlined clause below, what does 'it' refer to?
2) If a complement can be added to the end of the clause, what can it be?
3) As a whole, what does the underlined clause mean?

Her professors say that beyond an extraordinary mind,
what makes Alia special is a hunger to learn, a willingness to work hard,
and an emotional balance well beyond her years.
This would seem to be every parent's dream, but for a long time it was not...
By age five, Alia had finished the elementary reading curriculum at her Long Island public school.
By second grade, she trraveled to middle school for eight-grade math.