They actually looked at both. From the article:

>Microsoft is at pay parity when comparing women and people of color doing equal work with men or white workers, the data released Thursday also shows.
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>But the median pay figures — which measure compensation across the entire workforce regardless of title — show employees of color overall make less, indicating disparities between who is in higher-paying positions.

Reporting only whether there was unequal pay for people with equivalent role/title/etc. could also give an incomplete picture, as it's quite possible that a company pays everyone equitably for the job they're in, but still does a better job attracting, retaining, and promoting workers in some demographic groups than others.

In any case, I think a company reporting a mix of numbers is better than just reporting one, which could easily be cherry-picked to make them look good.