The primary reason for all of the non-Roman names is to hint that Latin can be used in the context of daily and modern life. Many of the contributors are from the Paideia Institute, which hosts annual living Latin conferences. I'll provide additional context/reasoning for the cities that I've encountered so far.
Philadelphía. Name of multiple Christian/Greek cities in the Roman Empire, and a major American city. I think that this name was used to show Greek loanwords and names in Latin.
Novum Eborácum. The original was a city in the Roman province of Britannia. The practice of naming cities with 'new' was also common in ancient times, with Constantinople even being nicknamed Nova Róma. I think they went with a city that had new in the name specifically to help show how adjectives change with their paired noun.
Bostonia. As far as I can find out, this is the only name that explicitly did not exist before the fall of the Western Roman Empire. It was likely founded in England during the late 11th century. Anyone able to use the UK National Archives can find Latin scans of documents mentioning Boston easily.
I must admit I find 'num' rather difficult to understand. Could someone kindly tell me how to say 'Surely you do live in Boston'? I shall be grateful. Or is it simply 'Habitasne Bostoniae'? I am beginning to wonder if the 'surely' in the English translation is actually needed. Donald S.
Nonne Bostoniae habitas?
While num expects a negative answer, nonne expects a positive answer.
Duolingo's use of 'surely' is just one way I have seen num and nonne translated. I have also seen translations like:
Num Bostoniae habitas? -> 'You don't live in Boston, do you?'
Nonne Bostoniae habitas? -> 'You live in Boston, don't you?'