Musical intervals are based on the ratio of two frequencies, for example an octave is a 2:1 ratio. Regardless of what those sound waves are traveling through, that ratio won’t change since the medium will affect them equally.
As far as universal harmony goes, it’s not entirely consistent across human cultures. Heck, even if you stick to western musical theory there’s a fair amount of variation. Though generally, small ratios (like 2:1, 3:2) are preferred to large ratios (like say 43:32). It’s not impossible that an alien would think about it the other way around though.
Now, for most people there is a bit of wiggle room, if the frequencies are close enough it’ll still sound alright. For example, in modern western music theory, only octaves have a perfect ratio and every other note is off by just a little bit, and it still generally sounds good.
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