I’m not sure what you mean by what is “actually there”? All we ever have is the observed phenomena. Perhaps I misunderstand, but when you say “they can’t make head of tails of what is actually there”, that sounds to me like you’re saying that the observed phenomena are not consistent with any of our intuitive mental models that are based on the macroscopic classical world. Notoriously, a photon is not “actually” a wave or a particle, although it can sometimes behave like either, and it can (loosely) be in different places at the same time. Under our current model, these observed properties, along with some others, fully define what a photon is. There may arise a more complete model, but it will certainly entail similar weirdness. The fact that this is startling and perhaps unsatisfying is not a failure of physics to explain what is “actually there”, it just means that our macroscopic classical intuition fails in the QM realm.
I don’t see any conceptual difference with the dark matter hypothesis. “Dark matter” is not an arbitrary name. The best hypothesis that we have to explain the data is something which know must have the properties of interacting via gravity (i.e. “matter”) and not by EM (i.e. “dark”). So “dark matter” states precisely the two properties that we do know so far. If the hypothesis is correct, we will eventually flesh out many more properties. And the sum of those properties will be all that it actually is. (I’m not excluding the possibility that the hypothesis might turn out to be completely wrong, although it seems unlikely.)