The correct position was obvious in 1787 and is obvious today. Congressional apportionment should be based on the number of registered voters. That would have excluded slaves in 1787. It would exclude noncitizen residents today. I have no problem with excluding minors as well; for purposes of apportionment, count them when they’re old enough to vote. They can be considered for other purposes from the point of birth, but apportionment should turn on voting eligibility.
And women. And children. And white males who did not qualify as voters. And free blacks who were not allowed to vote.
That is a fine idea. But at that time I do not believe they had voter registration.