The observation that a characteristic exists on a spectrum, and the observation that the vast majority of individuals fall on one of two extremes of that spectrum, are not mutually exclusive.

For the overwhelming majority of organisms, including Homo sapiens, all proposed indicators of sex (anatomy, hormones, cells, chromosomes) give the same answer. Reading the final two paragraphs of the paper, it's obvious that attempts to muddy this naturally clear water are being made for political, not scientific reasons.