Ah, I think I see the issue. Let me see if I have this straight.
1) According to the census and IGI records, Job/John Smith and Elizabeth Eagle had a daughter named Frances Palmer Smith.
2) There is a marriage between a John Smith and a Frances Palmer that would seem to be a good match for Job/John's parents and Frances Palmer Smith's grandparents.
BUT
3) Baptism records show that John/Job's parents are John and
Elizabeth.
4) There is a marriage between a John Smith and an Elizabeth Howard which would match with this information, rather than the John Smith/Frances Palmer marriage.
So, the question is, are John/Job's parents John and Elizabeth or John and Frances. If they are John and Elizabeth, why would he name his first daughter after a seemingly-unrelated Frances Palmer, rather than after his own mother?
Right?? Whew!
The theory of John Smith marrying twice, first to Frances Palmer, then to Elizabeth Howard
could make sense. But, you still end up with the same problem - if John/Job's mother was the second wife Elizabeth, why name his child after the first wife, who would be of no biological relation?
So, you are investigating the theory that Frances Palmer Smith was not in fact the daughter of John/Job and Elizabeth, but was taken in by them as their daughter (the fact that she was not baptised right after her birth would allow for this). She could actually be the granddaughter of John Smith and Frances Palmer, and is perhaps a niece or some kind of cousin to John/Job Smith.
In order to go further I think you need to find out whether the John Smiths who married Frances an Elizabeth are actually two different people. One way to do this would be to find evidence of some Smith children with parents John and Frances being baptised around the same time as John and Elizabeth's children.
Also, when I asked for Frances' father, I meant Frances Palmer Smith's father. Does FPS ever marry (it would be after 1851 since she is at home with parents then), and if so, who does she name as her father? If it is John/Job Smith then you have part of an answer. But if it is another male Smith, then we would have a name that we could explore further.
That is all the advice I can offer for now.
Let us know how you progress on this!
MJP