What set of system-wide configuration settings can conflict when installing different applications on a unix-based OS?

Reading this report on containerization the authors mention that: > A problem caused by Unix’s shared global filesystem is the lack of configuration isolation. Multiple applications can have conflicting requirements for system-wide configuration settings. I know that installing different applications for development, frequently different applications require different versions of the same libraries, or vaguely, that they require different system-wide configuration values. It is not clear to me what this set is on a unix-based OS. What configuration values commonly cause this issue? Naively, why is this not as much an issue once the application is deployed or installed by the end-user? Why is it that I cannot have the development build of similar applications running easily side by side, but I can download with a package manager and have them run with little or no problems?