After a quick search I would say the latter is more important here: what we observe from the bones are things like a quality of nutrition (e.g. vitamin deficiencies) or effects of some illnesses. Inadequate nutrition signals poor living condition and illnesses affect even the most "gifted" individuals (don't forget that hardship selects also for other traits than just a good immunity).
In Austria and Germany most people descripe the Nazi era also as “dark times”, despite there beeing roads built (although the Nazis were so in debt at the beginning of the war already that you can hardly call this a success).
So dark has multiple definitions. I thought the most.common one was about a time where rational thought and humanism didn’t really win, but tribal rivalry (on any scale) and radical beliefs did
The issue is that the Enlightenment wasn't a project to move human beings to some better plane, but to rationalize society and its members in a way that made it more amendable to control and planning. And so centralized power could use Enlightenment ideology to eliminate alternative power centers, centralizing power in the hands of a single state that could reorganize society for its own ends.
That itself had pros and cons, with the biggest con being the newfound ability for states to execute projects of mass violence more effectively.
London in the "Dark Ages" didn't have aqueducts. But Londinium was part of the periphery of the empire, and it also never had aqueducts. There's not that much information to be gained by cherry picking the elements of the central core of the Roman Empire and asking why they weren't present in far flung areas in the post-Roman era.
Skeletons show that people were relatively healthier (at least in the periphery) after Rome had fallen than when Rome had dominated these regions.