ciderdrinker - you have been a massive help with helping me in my research, it's been great discussing this family with you to try and make sense of everything. A fresh pair of eyes makes all the difference. Thank you.

I know we can't find absolute proof of the baptisms of John, William and Ann together with one family at the moment. It is possible that John and Margaret could be the parents, something for me to investigate further.
The fact that you have identified a very likely birth for Benjamin Brown in 1700 to a William Brown looks very good. So William Brown could be the grandfather of John who married Mary Saville. This has helped to narrow down the families to research considerably.
I have had a quick look at the family of William Brown. You mentioned you weren't sure if William Brown who married Dorothy was the only William having children at this time or if there were two families. I have done some research into this. I noticed a baptism for Johannes Brown 20/05/1715 to parents Gulielmi and Dorthy Brown in Abbots Bromley. Their other children appear to be baptised in the 1710s and 1720s. As my 6th great grandfather John Brown's brother William was born about 1729, I don't think William and Dorothy are the parents of Benjamin Brown.
I have seen an administration for a William Brown in 1707, Abbots Bromley. It lists his widow Ann and son Joshua Brown (he was of Bradley, Staffordshire). Also a William Robinson is mentioned. I found a marriage for this William Brown to Ann Robinson in 1685 in Lichfield.
I believe these are more likely to be the parents of Benjamin. Perhaps like you say Jonathan born 1704 could be John who married Margaret? I haven't been able to find anymore records for a Jonathan Brown.
Further research for me to do into William Brown and Ann Robinson and their children may lead to finding more clues to the parents of John, William and Ann.
Kind regards,
ALewis