Metaphor probably isn't the right word, but it's not really wrong either. "Placeholder" is also sorta correct but not entirely. Dark matter is a placeholder for an as-yet-unknown thing that interacts with gravity, in the most popular theories. There are less-popular ideas--still given serious study and consideration--like MOND that may some day explain the effects currently labeled as "dark matter". I don't think it's accurate to say "we know these are out there", and if it turns out that MOND or some other alternative explains observations, "dark matter" will turn out to have been fairly metaphorical (or just plain wrong).
We say "dark matter" rather than "weird gravity behavior" because the evidence thus far doesn't just look like gravity being weird. It looks like stuff, actual honest to God stuff, floating around. If MOND is right dark matter does not exist and never did. Dark matter is the name of the actual matter we believe is out there; we could be wrong, but it's not just a generic placeholder.
