WTF? In the map of current day they don't even include the great lakes. That was a major thing that happened recently with the carving out of the great lakes from the glaciers pulling back. The fact they don't even include them in the modern era shows how flawed this is.
Unfortunately that's how the data is provided [1]. Maybe because the Great Lakes were carved by geologically recent glaciation, and the model is built off tectonic plate movement.
A writeup of the methodology is available if you're interested. [2]
The maps are hand-painted representations of the various ages. On the earlier maps, there was a lot of care, but also unavoidably a lot of handwaving. For the 0 Ma map, I don't know if Scotese had a particular time in mind? It looks like modern coastlines, which means an interglacial period. A 100 ky average would be more glacial - the Boston coast would stick out more. I suspect he simply used the current coast. The absence of the Great Lakes, suggests it's not the current interglacial. A duration-weighted average of say the last 1 My of 10-ish interglacials might fade the Lakes to invisibility. So perhaps it's an eye blink of averaged interglacials, or a recent but previous interglacial, or a map rule like "don't include transient features", or a consistency of approach (eg, disregarding flavors of data unavailable for earlier maps, except for the coastline), or ... ?