I will need a couple of days to look at baptisms of James Atherton's in the early 17th C. We hold 'exact' transcripts of church registers recording people named Atherton but it is a paper based system indexed church by church and James is a popular first name. Computor based systems tend to have problems with unusual names and ignore little comments when they are attached to the entry because these are often written in Latin for some reason.
I am sorry to have been the one to have closed the door on the possibility of Humphrey of Winstanley & James being brothers. However, IF James was born in the Billinge/Winstanley area they will be to some degree related. In the year 1600 many Atherton's still lived in the clan formations that they have lived in during the late medieval. These groups are often descended from a single individual and in the case of the Billinge/Winstanley Atherton's, that was a man named Edmund Atherton who had been born in the Parish of Ormskirke and moved to Billinge as a young adult.