In English, we usually only put a possessive on the second person possessing - "Fratisek is Matej and Zofie's father" should be accepted (and afaik is actually the more correct version).
Using "a father" would suggest that Matěj and Žofie have more than one father; with "the father," it would be clear that František is their only father. But your comment raises the question of the possible acceptability of "a father" in the context of non-traditional families.