"I actually like having visible directories, versus having to figure out where in /usr/share or /usr/local/ or ~/.local or /var an installer chose to sneak their files in."
You seem to be mixing together two concepts here:
1. The files created by the installer, which are handled by the package manager. I can consult my package manager for files created by a specific package: pacman -Ql package_name.
2. The files created after installation (user preferences, plugins). The program should follow the XDG specification.
And those should be avoided as much as possible because they're always problematic and break randomly. How could they not break, when the package manager doesn't even know they exist or what they depend on?
1. The files created by the installer, which are handled by the package manager. I can consult my package manager for files created by a specific package: pacman -Ql package_name.
2. The files created after installation (user preferences, plugins). The program should follow the XDG specification.