Your post is a fundamental misunderstanding of the security model, but captures the part where software vendors are still operating under pre-Windows 2000 security setups. Interestingly, this happens not because Microsoft made it bad, but rather because every piece of software you use on Linux is a curated package distribution system maintained by an army of distribution maintainers whose sole job is to do exactly that--to modify upstream software to ensure it fits within that distribution's security model.
For example, Nginx on Redhat systems uses the "nginx" user, while on Ubuntu/Debian systems it uses "www-data". It's not like you're going to nginx's website, downloading binaries, and installing them manually and having to choose where to install them. It's curated.
You are operating in an extremely glorified and highly curated distribution-specific app store. Of course things are going to integrate a little bit better.