I thought Austria controlled Hungary during the time of the HRE, but it seems as if Hungary is not included in the borders. Konigsberg from Prussia, which belonged to Prussia, is also not included.
The Holy Roman Empire is not a standard Empire. It is more akin to a confederation of small German lands that are tied together in a confederation. While I can't talk about why or how it was formed, by the 18th century, Prussia and Austria (or rather the House of Hohenzollern and the House of Habsburg) gained lands through marriage. These were not counted as Austrian because they were crown lands of the House of Habsburg but it became known as Prussia because the Elector of Brandenburg was allowed to be called "King in Prussia" by the House of Habsburg because they didn't see any problem with him being a King outside of the HRE.
Generally, it's because the lands were tied not to the "nation" but rather the House of the controlling family.