The study links it to better metabolic health. Did you assume it meant worse?
I think they're saying that coffee is a healthier habit than soda.
Yes, my inference was "people consume caffeine, and if one group is getting it from coffee, the other group is getting it from non-coffee, mostly (highly-caloric) soda water, which explains why the coffee side looks healthier."
Makes sense, but I would hope the study design controlled for this, or designed around it.