It may be possible to confirm family relationships with Nathaniel by comparing test results with other
carriers of his Y-chromosome or his mother's mitochondrial DNA.
Y-chromosome DNA test-takers in his direct paternal line on WikiTree:
There's some conflicting info. in the records but you're right that he couldn't have been baptised before he was born.
Volume 4, Page 270
Early Records of Boston
[CHARLESTOWN.---Continued from page 184.
Hannah the daughr of William Smith & Anne his wife Smith.
was borne 27o.(7o.)1639.
Nathanael the sonne of Wm Smith & Anne his wife
was borne 25o(11o.)1640.
Mary the daughtr of Wm Smith & Anne his wife
was borne 20o.(10o)1642.
Volume 25, Page 339
The First Record-Book of the First Church in Charlestown, Massachusetts.
The year -- 1640 - - -
7th mo-day 27 Anna smith the daughter of william Smith and off
Hanna his wiffe -- was Baptized.
11th mo-day 3i- Nathaniell smith the son of william smith and off
Anna his wiffe -- was Baptized.
A note from Dorothy J. Smith (firstname.lastname@example.org)
Nathaniel wasn't born Nov 25, 1640 he was born Nov 25 but was baptized Nov 3, 1640 sister Mary b 1642 He was the 2nd child ,s/o William Smith a tailor from Charlestown, Ma. and Hannah/Anne. He married Elizabeth Ladd b Nov 1, 1640 d/o Daniel Ladd who came in the Mary and John March 24, 1633 and settled in Ipswich. then moved to Salisbury Ma and moved again to Haverhill, Ma before 1648. His wife's name was Ann. They had 8 children. I did find somewhere that he was b 1636