thank you for sharing your question with us in the community.
As for your questions:
1. They will give you, your passport usually back when your case is processed entirely. But in your case is slightly different, as regardsless of how the outcome of your asylum claim will be you will get an "Aufenthaltserlaubnis" through Familienzusammenführung. In this case you should discuss it with Freising.
2. As the Familienzusammenführung is applied through your wife in Heidelberg, they are responsible for the Aufenthaltstitel.
I hope I could help you, if there are further questions please do not hesitate to contact us in the community.