Yeah, that was the point. Jay is the doppelganger of Henry Allen, just given a different name because apparently his father left/died/something before he was born.
So if we're talking about trying to reconcile 1990 Barry Allen as another doppelganger, the fact that doppelgangers can have different names opens that door. Maybe Earth-1's Henry Allen, Earth-3's Jay Garrick, and "Earth-90"'s Barry Allen are all genetic doppelgangers whose father was named Henry Allen and looked like M. Emmet Walsh, and the Earth-1 version (and Earth-2, presumably) named his son Henry Jr. instead of Barry. (Although it would still be quite a coincidence that Henry and Henry Jr. both married women named Nora.)