And the package manager knows exactly where all the files are unless they are just config files, which are generally in .config or .local/share, and they are a lot easier than to track than the Windows registry.
Seems like "and so on" implies there are a bunch of places.
There are well-known places for well-known purposes.
Your house has a kitchen, bathroom, bedrooms, "and so on". You don't keep your car or skilsaw in the ones listed, but there is a place for each.