A birth certificate records the circumstances of a birth. The mother spot is not negotiable, it is reserved for the female person from who's body the child issued. This is an observable fact apparent at the time of the birth, as are other things listed on the birth certificate, like the place & date etc.
The birth certificate is not a DNA certificate, it is not a record of a person's genetic heritage.
Therefore the purpose of the father/second parent spot is not to list the gene supplier, but to record who is the second legal parent at the time of birth, ie. the circumstances of a birth
Adoption cases already have adoption certificates, they don't delete the birth certificate. In female same sex couples, it works well to list partner of the woman who gave birth as the second parent. In male same sex couples the process for an adoption certificate works well, it is very important to make sure the woman who's body birthed the child is not erased - because, again, the birth certificate records the circumstances of a birth