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I'd double check to see that chorus and flanger always start at the same modulation phase. It might be that the same file processed with the same settings will sound different, opportunistically, depending on how SoX manages the modulation cycles.

Re: Allpass, I don't believe a pure phase shift is perceivable, but I'd happily be proven wrong. Maybe it'll monkey with the transients.

It's not clear to me that a number of transforms, e.g. "bandpass filter," represent a monotonic dimension of variation, taking it quite a distance from the JND paradigm. We might reframe this experiment instead as "detection of common audio effects." Which is still likely useful.