Gilgamesh reveals that people who die in Singularities also die in real history too, they are just 'corrected' in
how they die. Instead of "a dragon ate this french peasant", they died due to the plague or something more mundane. Most likely, Roman didn't want to make Ritsuka or Mash feel depressed and guilty if someone died, so he carried those deaths for them as usual. Nasu says that Lion King's interference and Tiamat's awakening consequences were 'exceptions' as weren't the cause of the Singularity so they indeed got ignored and retconned, but all the rest stuck (so the final boss does have a super high death count with the many victims across time and space), which has some plot holes like how USA's founding fathers were all slaughtered by a bunch of magical celts led by Queen Medb so, what happened in history?
And as you said, Okeanus... I can give a leeway to Orleans, because a lot of people were killed in real life by famine, plague, wars, so likely that was the result of the dragon thing in the background. I don't think Nasu considered all ramifications in London, USA and Okeanus, though.
For simplicity's sake, in the anime, they just made some people survive and show them (while there were no survivors in game). Otherwise, trying to explain the obviously contradicting "check Nasu's blog to understand" world-building would be terrible for the conclusion.