You guys are trying to delegitimize a concept by using words like mystical mumbo-jumbo. You're not making an argument. Any sufficiently advanced technology is indistinguable from magic. Just because we can't understand it, doesn't mean its mystical mumbo-jumbo. The cipher is basically a language pack that allowed an individual to interpret a message recorded by an alien civilization.
I'd say that you're missing the point, but this is really on me for shorthanding it.
The problem isn't that the technology is advanced. The problem is that the technlology works, or sometimes fails to work, in a way that's convenient for the plot rather than a way that makes any sense. Shepard is getting sensory impressions after the first beacon imprint. This is OK for a sufficiently advanced technology , which can sort out the way a brain stores information. But why is it unable to sort out language if it can sort out sound and vision?
The answer, of course, is that the devs wanted to give us a hint of something rather than a burst of indecipherable static.