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You're contradicting yourself in your first and second paragraph...Those two paragraphs are talking about different OSs. 1st paragraph is talking about Windows, 2nd paragraph is talking about non-Windows systems with first-class package managers such as ArchLinux, Debian, CentOS, FreeBSD, etc.
> Those proper package managers still rely on the packager doing things correctly
Sure, but the point is you can query what the package manager has done.
> There's plenty of linux packages that creates files during operation in their designated /var/log/xxx /var/db/xxx /etc/xxx /home/xxx/ directories that you're not able to query using the package manager.
That's half true. You can query that /var/db/xxx and /var/log/xxx has been created by the package manager and often the directories (and their contents) will be owned by the user which the daemon runs under.
However I do agree with the point regarding your $HOME directory and actually made that point myself:
> Of course you still have the problem of the software writing files during its operation but that should be limited to $HOME (on POSIX systems) or any path that is writable by the owner / group of the user that application runs as (which should be limited even if it’s a system service).
As an aside, you can also query what files a particular application has open. In fact there are a few ways to do this from querying the /proc/$PID directory through to tools like `lsof`.