This is presumably the John "Gater", age 15, who emigrated to Virginia in the company of John Gater, age 36, and wife Joan,age 23. Obviously he isn't Joan's son (she would have been too young), but he may have been a son from an earlier marriage, or a nephew, or perhaps a cousin (nephew is more likely, though).
Whether he is also the John Gater, wife Mary, who removed to Anne Arundel County, Maryland, seems to be a matter of opinion, as is whether Mary was a Waters/Walters or not.
He was apparently *not* the John Gater/Gaither who helped found Abington, Maryland - that was a John Gaither in the next generation.
Some genealogical theorists write him off as a dead end, who either died in Virginia soon after arriving or bugged out back to England at his first opportunity. These theorists assume that Joan Gater died and John Gater I (not II) married Mary whoever.
Apparently there was a nasty mess-merge at some point, and sorting it out has left various loose ends.