Yes, though broadly changes in eustatic sea level are one of the things that we attempt to account for when making paleogeographic maps and as mentioned in the original answer, depositional environments can provide some context to the location of coastlines, etc. That being said, the point is valid in that paleogeographic maps tend to be amalgamations of time periods, i.e., at the finest scale we might make a paleogeographic map that represents the "average" of a few tens of thousands to few million of years of time and certainly within that you would expect a decent amount of sea level variation. All and all, a paleogeographic map would give you a rough approximation of things and would be better than nothing, but yeah, you would need to expect it to be pretty wrong at times.