The Minor court doesn't say that solving doubts about whether these person are citizens or not would make them natural-born citizens. In context, it has already say they are not. Natural-born citizen was used to exclusively characterize one class of persons. If the second class that you cited could be natural-born citizens, then the court had no reason to reject Virginia Minor's argument of being a citizen via the 14th amendment. What other point does it serve to talk about being born to citizen parents??
The fact remains, Minor v. Happersett has been presented to the Supreme Court of the United States in several Petitions for Writs of Certiorari as cited precedent in Obama eligibility appeals, to no avail.
Twenty-four years after Minor was decided, the Supreme Court ruled that:
[An alien parent’s] allegiance to the United States is direct and immediate, and, although but local and temporary, continuing only so long as he remains within our territory, is yet, in the words of Lord Coke in Calvins Case, 7 Coke, 6a, strong enough to make a natural subject, for, if he hath issue here, that issue is a natural-born subject”