This is usual in history. They have some sources and try to do their best effort to make a reliable map. [I'm not a historian, so I can't be sure how good is this map.]
When you see a map of Europe in 1000AD, you have almost the same problems. Europe is easier because they had a written record, and some map from that epoch. Anyway, the historical records may be wrong due to political reasons ... so it's not easy.
Another point is that maps changes with time. The map of Europe in 1000AD, 1100AD, 1200AD, 1300AD, 1400AD, 1500AD are different. The maps of America in the same years should show the change of the territories each one had.
I've never heard of this before. Does anyone else find it strange that two very strongly Catholic societies abandoned the Latin version, while other societies didn't?
I think abandoning ecclesiastical Latin terms for things is kind of random, and isn't usually very correlated with religiosity. (If people actually wanted to be secular about it, they would nowadays say "era volgare", "era comune", "era comum", etc.)
Edit: for example Portuguese has retained numbered weekdays (like Hebrew and ecclesiastical Latin practice), while Spanish has gone along with the widespread European trend of using the classical Roman names. In Spanish the first work day is the Moon's Day, while in Portuguese it's Second Day (based on the Biblical second day of creation).
Given that we're fast approaching the 500th anniversary of Martin Luther's famous door-nailing, the roles of vulgar languages and schism with Catholic doctrine might be related to this, though I'd have to look into the history.
The AD/BC system is formally known as the Dyonisian Era System, and dates to ... 525, er, CE, when it was created by Dionysius Exiguus.
The use of "common era" dates to 1615.
The English Reformation (schism with the Catholic Church) to 1532 - 1534.
Well let's just say the period immediately predating the European invasion, that generally occurred starting around the 1600s in North America. Of course this isn't static but the perspective is important because a lot of displacement occurred post contact with Europeans and a lot more warfare and disease resulted. The perspective this map provides could be compared to a post contact map of tribes to highlight the many migrations that occurred.
Europeans contacted different areas at different times, and I can imagine some of these areas and borders changed. It's probably going to be a rough approximation no matter what you do.
That's no reason to belittle this effort, though. There's enormous amounts of information on that map, and even if it's not 100% perfectly accurate, it's still way better than what we had before.
