It doesn't. In fact, if it worked as you expected it would break SOLID
it's definitely a serious design flaw
Sorry to be brutal: No, it's not a flaw, you just didn't understand the design of model/views.
To help you get a better idea of what is going on, try use the same model with 2 different treeviews. In only one of the view call setRootIndex, and then trigger the filtering.