I'm not sure I agree that most uses of Linux are single-user. I know this (likely) isn't what you meant, but at a minimum most every system, even containers, will have at least two users: root and the non-privileged user account. It may not be two humans but it is two users. On my current desktop (where I'm the only human user) I have 53 entries in /etc/passwd. Each have different permissions and access to resources.

But even if you consider the above to be a single-user setup (which is reasonable) I still think there's value in consistency. I personally get a ton of value from having CentOS and RHEL systems being laid out the same as my Fedora Laptop and Desktop system, and having all that knowledge transfer both ways. Being able to add a user to a "single user" setup too is very useful. It would suck if adding a second user required completely changing everything about the filesystem.

FHS makes sense from a system developer standpoint — entire system is a project

    /lib for libraries
    /usr/include for C includes
    /etc for configs