Why is it that the parish of residence is often shown on other folks' entries but rarely on mine?!! Careful though! The marriage entry shows he was of the parish of Kempston, which doesn't necessarily mean he was born there (but in this case he probably was!).
Who were the witnesses at the marriage? Do they provide any clues? Siblings perhaps.
There's a burial in Willington on 14 Apr 1830 of John Goodden age 64, which is spot on for a baptism on 17 Nov 1765. Checking the IGI, which for Beds baptisms pre 1812 is almost 100% extracted, there's no other John Goodwin which would fit, so I think you're pretty safe in assuming that he was the son of Nathan and Ann.
If you wanted to do a belt and braces job you could check Kempston transcript to see who the John Gooding was who was buried there on 3 May 1784, to make sure he wasn't son of Nathan, and while you're at it look to see if the banns were entered in the register (there's an IGI member submission of a marriage at Kempston on 6 Apr 1788 between John Gooding and Frances Woodriffe, and I wonder if this actually relates to the banns - although they are only valid for 3 months)
For Nathan and Ann's marriage check the IGI under GOODIN, rather than GOODING or GOODWIN
David