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It is done for exactly the same reason the mains transformer and output transformer of a typical valve amplifer have their respective laminations arranged mutually at right angles. Depending on the skill of the transformer design, especially that of the laminated core, the flux leakage will be small. But the inductors used in loudspeaker crossover networks are often 'air cored', so the flux is poorly contained and thus, unless the coils are arranged at right angles to one another, can cross-couple.
Inductors that use ferrite cores are better in this respect, but are disliked by some.
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Given that the inductors in crossovers are usually quite small they would have to sit very close together for any interaction to happen.
I don't recall ever seeing a crossover where this might be a factor not even very cheap speakers. probably because it's a known potential issue and costs nothing to avoid.
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Is 90 degrees to adjacent inductors the optimum orientation angle?
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There are many different ways to arrange the 90 degrees.
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