If there are structured radio signals being emitted, it matters not whether or not we understand what the aliens are up to, if it hits a sweetspot between noise and simplicity we can tell it's a signal. And no, "radio waves" aren't the equivalent of "smoke signals", if there are better ways to communicate across space, that would change a lot our understanding of physics. This isn't to say that our understanding is complete, but the default assumption should be that it's very unlikely that there is a better way to communicate long distance.
Compression is an issue in that respect, but that's a different argument.