1) Nothing. This is as designed; FireBreath installs per-user by default, always has. This is a feature, since it means you don't have to have administrator privileges to install.
2) Not by default, no.
3) Uncomment the following line in your PluginConfig.cmake file and rerun the prep script:
# If you want to register per-machine on Windows, uncomment this line
set (FB_ATLREG_MACHINEWIDE 1)