I think that "zur Universität" is a dative prepositional phrase describing place. That means that "in Berlin" is either
- the same, or
- an accusative prepositional phrase describing place, or
- Dative indirect object
If it's the first, then I don't know the rule that says why it comes before "zur Universität".
If I rewrite it as
"Meine Tochter geht zur Universität. Die Universität ist in Berlin." Then "in Berlin" is clearly a dative prep phrase describing place.
I half-remember a rule somewhere about ordering things in the order of least specific to most, which might apply here.
(But I also know that "zur Schule" is a special case; you'd think it would be accusative since it works with geht, but it just isn't; similar situation with "zu Hause".)