Well I've read the first paragraph and I'll stick to my earlier point : he mentions the non-agression pact and at the risk of being pedantic and splitting hair speaks on the dual invasion. To me that opening bit is more or less clearly about the armed push itself, the initial occupation or maybe up to Barbarossa until which both had approximately control over half the country. I'll add that unless there's some later part of the article where this passing mention of the Soviet Union occupation of Poland comes into play, it strikes as a bit of context for 1939 and I don't find especially controversial to say the Soviet invasion of Poland in 1939 was "as murderous" and the Soviet and Nazis shared a commonality of intents in that specific case : After all, they planned it together, did they ?
It's pretty farfetched to see this as Holocaust denialism even "soft" and to make an argument via hyperbole it's a bit like saying that the Soviet aligned states body count is astronomically higher than the Nazis and that it's denialism promoted by cultural Marxists in universities yadda etc tutti quanti. Brushing aside the exactitude of the numbers, while Marxist Leninist regimes have an horrible & terrifying record it's obviously a bit of a brain fart to compare in absolute terms the two because of the wildy different timespans, areas and populations concerned (and intent, specifics, etc...)
It's reading a lot in a sentence to think that "murderous" really means "numerically comparable" and up to "numerically comparable from September 1939 to May 1945". Especially since the NYT allowed me to take a glance at the article and I don't have the impression this bit is really more than that : a bit.