@KZO I was reading that thread (https://mangadex.org/thread/191519/), and it appears that for the time being, they're waiting until the site overhaul, so for the present at least I'm trying to categorise by the old separate distinctions.
@Alex-S the terms mean a lot of different things to a lot of different people. In short, your assumption that "shoujo ai" is largely a USA/Western fan construction is true, but the terms are used differently. "Shoujo ai" tends to refer to lighter girls' love stories (sometimes "ship bait" or "yuri teasing") where there's a lot of implication, but no actual "action". Think things like Hibike! Euphonium, a lot of the Manga Time Kirara catalogue, and the vast majority of titles that are often also called CGDCT. "Yuri" then, tends to refer more specifically to titles with actual confirmed romance. Think Yagate Kimi ni Naru, Kase-san, etc
As you've noted by implication, in Japan there's no distinction, they're just all called yuri, so I've been currently left unsure what tag to use under the current system. When the Mangadex redesign happens this will be a moot point, but for the present, I've been doing my best to think about proper categorisation.