Do you think the nytimes was respecting that difference? Nothing else really matters for this.

I think the previous poster's point was precisely about the vernacular - don't forget the flags in the articles derive from news headlines, of which the vast preponderance are very much expressed in the vernacular.

Speaking for myself, growing up in the 80s, I definitely wasn't completely aware that Russia and the USSR were separate concepts, probably until the latter's break-up.

You're starting with the concept of "Russian SSR" to mean "Russia" and going from there, and this line of reasoning makes sense. But really, "Russian SSR" was the novel concept. Before the USSR, "Russia" meant the "Russian Empire", which comprised of basically the same area as the USSR. So during the time of the USSR, "Russian SSR" had no meaning (to the West), it's only significant now in hindsight after the breakup. To summarize this perspective I'd view it like this: The "Russian Empire" i.e. "Russia", was renamed "USSR" and internally they drew lines to make states, for which "Russia Core" for lack of a better name was simply called "Russian SSR".