Did he have any siblings for whom you've found their baptisms. I only ask because my gran was one of 6 children and I found 5 baptisms but not hers, so I looked at the baptisms of the child older than my gran and the one younger and found they were baptised at the same church (different times), so I looked on Ancestry for that church around the date of birth of my gran. I found her baptism, but instead of putting her name down, the parish clerk (I presume) had written her father's name down instead of hers, whilst also writing her father and mother's names in the correct box. Of course, that also meant that she had gone down as male.
As I knew my gran - she lived with us until she died - I know she was definitely female having produced 10 children, 2 died as babies, one as an adult with TB, but the others, my mum, my aunts and uncles I knew too.