Again though, you need to have some sort of base data to begin with, and a 1399 startdate is simply not going to give you the kind of demographic data you would need to have any confidence in the numbers you do enter for those provinces, not just in RoTW but for large parts of Western and Central Europe as well, to be able to include the rural countryside along with cities.
Sometimes you simply have to accept the limitations that data contain when you make your models.
But would those population figures have to be historically correct?
What matters, from a gamist perspective, is that there is some number, and that that number changes dynamically over time, with consequences for income, manpower, etc. Would it really ruin the game if that number didn't start at something historically correct?
Historical demography is an established science, and while its results are calculated estimates, the game wouldn't need any higher accuracy than, say, no value being off by more than a factor of 2 or so.
Then the game could actually model the consequences of things like depopulation of territories through war, as happened to Germany during the 30 years war.