I had a very similar problem a while ago: I wanted to store local dates on the server side (i.e. just yyyy-mm-dd and no timezome/time information) but since the Angular Bootstrap Datepicker uses the JavaScript Date object this was not possible (it serializes to a UTC datetime string in the JSON as you found out yourself).
I solved the problem with this directive: https://gist.github.com/weberste/354a3f0a9ea58e0ea0de
Essentially, I’m reformatting the value whenever a date is selected on the datepicker (this value, a yyyy-mm-dd formatted string, will be stored on the model) and whenever the model is accessed to populate the view, I need to wrap it in a Date object again so datepicker handles it properly.