I think we’re basically on the same page. As you note, a conserved promoter without strong sequence conservation elsewhere suggests functions that might be more

I think we’re basically on the same page. As you note, a conserved promoter without strong sequence conservation elsewhere suggests functions that might be more structural or regulatory. Still, it’s also true that some (actually many) non-coding regions show no evidence of selection and appear to evolve neutrally. To borrow an example: an onion likely doesn’t need 5x more DNA than a human, and a lungfish probably doesn’t need 30 times more than we do (and 350x more than a pufferfish). And yet, these enormous genomes exist. It’s very likely that portions of these sequences are what we’d call “junk,” i.e., DNA that doesn’t confer a meaningful functional advantage and can accumulate due to the relatively low cost of carrying it along. If we want to avoid the term “junk,” we could say something like “areas of the genome for which we assign a very low prior probability of functional importance.” But “junk” is a concise shorthand to acknowledge that, while some non-coding sequences matter, there are also huge swaths of DNA in many eukaryotes that show no signs of being anything other than evolutionary baggage.