Aren't dot files just pretending to be hidden due to a bug in early Unix?
Unix v1 had a flat filesystem. Unix v2 added subdirectories. As an implementation detail, each directory contained two magic files, `.` for "this directory" and `..` for "the parent directory".
The command to list files was sloppily coded to skip them. If a name started with a dot, it was skipped.
Hey presto! Unix 2 had a way to hide files! It was a bug, but it was useful, so it stayed.
So, Gobo doesn't use `/etc` and `/var` and all that 1970s nonsense, but it keeps them around, empty except for shortcuts, for sloppy code that assumes they are there.
But they are hidden, just like dot files are hidden on every Unix-like OS. Because it looks better, no other reason.
Fair enough, it's a mess mostly due to old conventions, the LSB, etc. I would be more satisfied with a kernel or init system or whatever that can configure where libraries are, temp data, cache, local software, system software, global configuration, etc. Then the primary difference in pathways for Gobo vs, say, Debian would be what paths they configured for Linux's main types of OS data.
It would make playing with alternative hierarchies kinda fun.
Playing with alternative structures is fine though.