Huh, he drew PC-98 versions of Reimu and Marisa, but Windows Yuuka.
It's because Touhou girls store their identity in their headwear. Reimu's always identifiable if her hair tubes are visible, as they are here. And Marisa's got her hat. But Yuuka doesn't typically have anything on her head, so it's harder to identify her if the outfit's different than the usual. Hence, Using the more-common Windows version as a compromise.