I've just been reading The Time Travellers Guide to Medieval Britain by Ian Mortimer, which covers 1300-1400, but the city, town and village sizes aren't that far off what's given for The Empire, but there would be many, many, many more villages, even some of the more detailed maps done of The Empire (Excluding all the issues I have with maps of the Empire) have a few massive cities, and a handful of surrounding villages, and occasionally a few small towns and villages between each city. In effect they have some kind of settlement every 25-30 miles along major rivers, and not much else. In our world there would be some sort of settlement every 5-7 miles along those trade routes, and even out in the surrounding area - obviously we don't have such bizarre things to deal with as Forest goblins, beastmen and elves, so I can sort of get there being less density away from major routes, but only so that along those routes there would be more density.
I'm currently reading one of the following books The Time Travellers Guide to Restoration Britain 1660-1700, which is much more in keeping with the period of the Empire technologically at least. I don't know enough about central European - German history to know when the Holy Roman Empire period was. Anyway, population is only around twice that as it was in the 14th century.
Regardless, my way of reconciling the differences between WFB and WFRP, for when I'm GM'ing WFRP is to multiply the size of those settlements listed in Sigmar's Heir's by 10, and assume there are smaller villages in between