If everything is managed by the package manager, there is a database of files that are installed, and assuming the package manager works correctly it shouldn't

If everything is managed by the package manager, there is a database of files that are installed, and assuming the package manager works correctly it shouldn't create any problems. I use installations made 10 years ago and they are perfectly fine! Different is for software that is not installed by the package manager, that in Linux is typically installed in /usr/local (if we talk about stuff that is compiled, or installed by another package manager such as pip or npm) or to /opt (for proprietary applications distributed as a binary).