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Zig Zagged: A team is deployed to Germany because surveillance photos show Nazis with highly advanced technology, only for them to turn out to be fake once they get there, however it later later turns out that the Nazis have occult mystics capable of wielding powerful magic and/or Magitek. And THEN it turns out it's superscience after all.
Averted: Wehrmacht is just Wehrmacht. Nazis are just Nazis.
Enforced: "Simple Nazis are not threatening enough! We have to play up their technological developments!"
Lampshaded: Holy shit! That Nazi Superscience is nothing like i've ever seen!
Exploited: The Allies salvage and/or steal the products of Nazi superscience to reverse-engineer them and make their own.
Space aliens passing by see what Hitler is up to. They proceed to discreetly stomp out any and all viable superscience projects, leaving only impossible ones which will further weaken Germany by chugging up it's resources.
Germany's lack of resources, intellectuals migrating to the Allies instead of facing anti-semitic persecution, Hitler dismissing the New Sciences as "Jew Sciences", and the general Jerkassery of the higher-ups almost make it impossible for game-breaking superscience to make it past the planning stage..... just like in real life.
Conversed: "Oh look, it's Stupid Jetpack Hitler again. It's so damn egregious!" "You do know they actually were ahead of time with many inventions in Real Life, right?"
Deconstructed: In something similar to what happened in real life, what the Nazis gain in a power advantage from their super-tech they lose in mobility and resources. While immensely powerful, the Nazi superscience is incredibly expensive, resource-intensive and time-consuming to produce and operate (sometimes relying on incredibly rare or unique Unobtainium), is difficult (or impossible) to mass-produce, is slow to mobilize and is easy to attack or sabotage. Meanwhile, the opposing armies have much less powerful machinery backing them up but are able to quickly produce and mobilize more of it. This means that if / when the Nazi superscience is knocked out on the field the Nazis are significantly disadvantaged, and the drain on their limited resources caused by the super-tech means they are unable to easily produce replacements, thus putting them in a likely position to lose the war.
Reconstructed: Some people in the Nazi high command are Dangerously Genre Savvy, and instead of putting the superscience into building wunderwaffen like Death Rays and Walking Tanks, they put it into improving the industry and economy. With factories that produce more and more tanks while wasting little to no resources and power plants that don't need coal and oil to run, the Nazi war machine can produce near-infinite reinforcements, forcing the Allies to invent new tactics... or die trying.