For the most part, Austria, Hungary, and Poland are broken out separately according to their present borders, even for the periods when they weren't separate countries.
Maybe I misunderstand what is said on page 16, but to me it seems like foreign nationals like Polish people are included in other countries data. So the data is bound to geographical areas not nationalities, while the interactive map shows today's geographical boundaries, which don't included said geographical areas and nationalities anymore, making the data skewed.
How was the data gathered? Depending on what you asked a Hungarian from 1850, you might have gotten 3 different countries.
The footnotes on page 11 give a good explanation.
For the most part, Austria, Hungary, and Poland are broken out separately according to their present borders, even for the periods when they weren't separate countries.