Went back to look at the Flixton registers again!
Flixton registers vol. 1 (1570-1730)
Kelsalls - only two entries
27 Jan 1725 Baptism Jonathan, son of Jonathan Kelsal, born 4 Jan 1725
31 May 1658 marriage John Mather to Margery Kelshawe
so your James Kelsal that had the child with Mary Penny, he wasn't baptised at Flixton.
Penny surname
There were a lot of Pennys in the earlier volume, far more than I could write down! The earliest was a baptism for Elizabeth Penny, daughter of Thomas Penny of Carrington, 21 May 1659. Most of the Pennys gave abode as Carrington. The name Thomas gets used over and over through the generations, There wasn't an obvious parent for your Mary Penny, so the Mary baptised 1719 at Bowdon is still looking the best bet.
Trouble is, because the Pennys are long established in Carrington, and use the name Thomas over several generations, I think it weakens the case for your Mary Penny being a grandchild of Rev James Penny of Great Budworth. There were two Thomas Pennys baptised in Cheshire in the 1690s:
Thomas son of James and Ann, Great Budworth, 12 November 1692
Thomas son of Thomas (no mothers name), Bowdon, born 10 Aug 1698, bap 29 Aug 1698
I think geographically, the Bowdon one is more likely to be Mary's father, and he can't be the vicar's son as the vicar died 1694.
However, going back to Family Search, if you look for baptisms of children, surname Penny, father Thomas, in Bowdon between 1715 and 1735, there are some with parents Thomas and Mary and some with parents Thomas and Alice. So there might well be two Thomas Pennys in Bowdon to choose from!
Does the vicar's will mention anyone in the Carrington/Bowdon area? If so he might still be a relative as Great Budworth and Bowdon are only about 12 miles apart.

Barbara