I don't understand what that mean, "the baptism record gives the father's surname, not the child's." The very definition of hereditary surnames means that these are the same name. It gives their common surname, no? Although baptism records usually put that name once, right next to the father's call name, it is absolutely clear to me that it is the name being given to the child as well.
On the other hand, a modern birth certificate would name both a father and a child. On a very rare occasion, those names might be spelled differently -- but because of error. And Wikitree policy does account for using a different spelling for LNAB other than that on the birth certificate if there is cause to believe there was such an error. But it does not view a particular spelling arising from being recorded at a time of non-standardized spelling as being an error.