Doing an individual PhD in Germany from abroad
This question is very difficult to answer in general as PhD programs and their rules are hardly standardized in Germany, every university can mostly do as they please.
In my research institute (STEM) PhD students are employed workforce and as such your contract cannot start before you present yourself to HR at least once in person. But this does not seem to be the case for you.
During these Covid days many rules have also changed or are temporarily not applied. In my experience, the administrations have become very relaxed, allowing many things that were not permitted before. For example, a friend of mine was able to receive the written assessment of his thesis by email, vowing to delete it again, while normally it is strictly required to read it in person, under supervision and the strict ban of any recording devices.
As such, in general, if your supervisor agrees to you staying in your country as long as Corona is around, there will probably be a way to make it happen.