Answers
Τhere is no reason to worry about this issue. The coronavirus situation is a force majeure phenomenon globally. There is no need to prove the existence of the above situation. According to existent jurisprudence, the periods of such force majeure situations are not counted in the finally calculated periods of absence. From the passport exits/entries, it is proved that it was not possible to return on time.
Your temporary absence form Greece will not be a problem for the time being.
Physical presence is essential as far as the application for Greek citizenship in general. Acceptance or denial will not be justified otherwise could be subject to appeal.
This can delay a bit your application for citizenship,
In order to apply for citizenship, you should live seven years continuously in Greece, which means that you should stay in Greece for 10 months each year.