Yes
Edit ~/.config/mimeapps.list and place the atom desktop file as the first entry for the desired file types.
You can also use xdg-mime to set default application for specific file types - but editing the mime file is probably the quickest.
No (maybe) because writing files in write protected locations requires superuser permissions.
Some applications are gvfs compliant - in which case the admin: protocol will work - which means it is using pkexec to launch the editor.
Only a subset of text editors supports gvfs and gvfs doesn’t work well with KDE.
If your i3 system uses Thunar you can create a custom action when right clicking a supported file type.