Installing each package into it's own directory, and maintaining symlinks into that directory structure, was an approach explored for large system installations in the 90s and 00s.
NIST depot, Xheir, CMU, and Nix all did this in varying ways. The advantage of this approach was that packages could be installed once on an NFS, scoped by version/configuration, and mounted into the filesystem of every work station on a campus. The workstations then just needed to maintain references to the files on the NFS for their particular software configurations. There is also some interesting exploration of composable configuration templates that allow workstations to inherit and extend a particular configuration (i.e. the physics department might have a base template).
Nix is easily the most successful in this space. It even uses something similar to the NFS approach! It can maintain a remote cache of observed configurations to pull from instead of redoing work.
Reading these LISA papers is a lot of fun. If you work in system administration (i.e. maintaining an Artifactory instance for your company) and have a day to spare - I'd very much recommend reading them, starting with the Nix paper!
To get you started:
Nix - https://www.usenix.org/conference/lisa-04/nix-safe-and-polic...
Depot Lite - https://www.usenix.org/conference/lisa-viii/depot-lite-mecha...