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They know that folding space works according to a model that's supported by empirical evidence. That's about as science as it gets.

If some deeper understanding of the metaphysical nature of the universe were required for FTL travel, that would be magic. But that's not the case, they have an equation that works, and they can use it without even knowing why it works.

We built airplanes, broke the sound barrier and put people on the moon when our theories of aerodynamics couldn't explain how a bumble bee could fly. Would you consider airplanes that were built without a complete understanding of aerodynamics to be magic?