Might I suggest that extermination of Jews did not fit into their "both sides do it" template, and so was never specifically mentioned?
I have no problem with such perception as a hypothesis from which one begins researching the matter.
However, if a decision is made to research press reports of the period, clippings from the NYT mentioning other reports are not the substance of which hard beliefs should be based. One really needs to research the original Vatican and other agency releases the NYT occasionally paraphrases.
Bear in mind, FDR was largely silent on the subject and wouldn't accept Jewish refugees. FDR was also silent on the subject of treatment of American POW's by the Japanese. He even had the media spike stories of Japanese atrocities handed them by MacArthur.
In all fairness to FDR, he did order as many Jewish refugees as were allowed by law to be accepted -- and indeed, the vast majority of refugees legally entering the United States in those days were Jewish.
FDR also worked to find other homes for Jews who could not come here.
And in due time, as data escaped from the death camps, President Roosevelt joined with Churchill and others in denouncing Nazi atrocities.
But, more to the point: in the grand moral scheme of things, I doubt if it's wise to attempt justifying the Pope's behavior by pointing to analogous behavior of some American politician.
Surely, no legitimate moral equivalency exists?
Finally, I have no doubt that the Church then, just as we do today, found it near impossible to draw moral distinctions between Hitler's Nazis and Stalin's Communists -- who can even say today which of the two murdered more innocents?
Indeed, which murdered more of the clergy that fell into their hands?
So "fair and balanced" criticism was not just some abstract ideal, it also reflected reality of the time.
The great exception was the systematic extermination of Jews, as Jews, which had no moral equivalent elsewhere, and so far as I know was not mentioned publicly by the Pope.
At least that's what "most historians" who've studied the matter tell us...