Hi, I think that without an obvious change of subject the "ability to leave" or the desire remains with "Ella". I guess you could add the pronoun "Yo" before the quiera to convey your meaning, but I still think it sounds a little strange or incomplete in English to say, She can go when I want. Maybe she can go when I want to. Or she can go when I want her to etc. Whereas she can go when she wants needs nothing adding to it.
Yes, if it was the usted form. Usually the "usted" is included in the sentence.
Duo probably just hasn't added that to their database of correct answers because without the usted being written in the sentence, it's probably not usted but rather he or she.
Also, the most straightforward translation of this sentence would be without a subject change, so in the contextless world of Duolingo it's best to go with the safest translation. SHE can go whenever SHE wants.