Internet doesn't work with proxy client installed

Enabling Tun mode asks for this:

pkexec /usr/bin/chown root:root /usr/lib64/Throne/Core
pkexec /usr/bin/chmod u+s /usr/lib64/Throne/Core

It should keep the privileges unless you reinstall the package.

If the issue persists, try using a workaround:

sudo tee /etc/polkit-1/rules.d/00-pkexec.rules << EOF > /dev/null
polkit.addRule(function(action, subject) {
if (action.id == "org.freedesktop.policykit.exec"
&& subject.isInGroup("wheel")) {
return polkit.Result.YES;
}});
EOF
sudo systemctl restart polkit.service

I use split routing with IP sets by GeoIP for Tor running on the router, which applies to all LAN clients, so I don’t really need desktop proxy apps.