Probably yes. FDR was aware of the Japanese threat, (which was part of his motivation for cutting off oil) but he was personally more oriented towards the European theater.

Also, keep in mind that while Germany and Japan were technically in an alliance, it wasn't a close one, partly because of differing goals and partly because of the sheer distance between Europe and East Asia. So while they were on the same "side" (mostly because of having common enemies) and had diplomatic relations, they didn't share much intelligence or really coordinate. Which makes sense, because neither was much interested in things happening on the oppposite side of the world, far beyond their respective spheres of influence or desired conquests.

So in a scenario where the Allies push the Germans back to Germany but come to a mutual anti-Russian truce, the Japanese would not be part of such a truce, and would continue fighting. Assuming that Pearl Harbor plays out similarly, America would still fight and win the Pacific War again. Realistically, the only scenario where the Japanese maintain their massive empire is one where they don't start a war with the U.S.

Australia would be a bit of a wild card- in our timeline they also fought the Japanese in Indonesia and Southeast Asia, but with aid and intelligence sharing from the U.S. Japan would never be able to conquer Australia, but could theoretically bomb it or attempt an invasion. And Australia might be able to make significant inroads into Japanese holdings without American help. That brings in way too many new variables so I don't know how a Japan-Australia war would ultimately play out.