Having graphical/GTK applications started under sudo is a security issue, the fact that you know some example of program doing so doesn't make it a good idea. The right way to give access to user-restricted action would be through polkit integration (which is what update- manager, software-center, control-center gnome-disks, etc are doing) and not by having the UI being under privileges as well.
In any case feel free to report that bug to GNOME since they are the ones writting nautilus, Ubuntu is not likely going to look at issues from non recommended usecases ** Changed in: nautilus (Ubuntu) Status: New => Triaged -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to nautilus in Ubuntu. https://bugs.launchpad.net/bugs/1502706 Title: Nautilus failed to create $HOME/.config/nautilus when it is run as root when HOME=/root Status in nautilus package in Ubuntu: Triaged Bug description: As title, Nautilus failed to create $HOME/.config/nautilus when it is run as root when HOME=/root ProblemType: Bug DistroRelease: Ubuntu 14.04 Package: nautilus 1:3.10.1-0ubuntu9.9 Uname: Linux 4.1.4-ck1-1000hz-nehalem-preemptive-bfq-uksm-iommu-simplefb i686 NonfreeKernelModules: nvidia ApportVersion: 2.14.1-0ubuntu3.15 Architecture: i386 CurrentDesktop: KDE Date: Mon Oct 5 04:37:45 2015 GsettingsChanges: b'org.gnome.nautilus.list-view' b'use-tree-view' b'true' b'org.gnome.nautilus.list-view' b'default-column-order' b"['name', 'size', 'type', 'date_modified', 'date_accessed', 'owner', 'group', 'permissions', 'mime_type', 'where']" SourcePackage: nautilus UpgradeStatus: No upgrade log present (probably fresh install) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1502706/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp