Nothing should ever be installed or stored on the root of a system drive. Blame the app developer for not adhering to standards.
*nix systems (Linux, macOS, BSDs, etc.) have a file system hierarchy already planned out for this. The apps should be utilizing this system:
https://unix.stackexchange.com/a/114480
Linux file system hierarchy (macOS is basically the same):
https://tldp.org/LDP/Linux-Filesystem-Hierarchy/html/usr.html
Even Windows has rules & guidelines for proper app installation where nothing should be on the root of the system drive.
Just because it can technically be done (installing or storing to the root of a system drive) doesn't mean it should be done.
Besides it is the user's responsibility to make sure all their third party apps are compatible with a new version of macOS before upgrading macOS.