Unless I've missed something, there's currently no immediate way to identify when a site's using custom "Website settings" — instead I've got to expand the Gear menu (or select Orion > Settings for X)
Could a small badge (top right dot) be added to the Gear icon as a signifier that "something's different with this site"…? Unfortunately, unlike the Star icon (for Bookmarks) there's no filled, or any other type, of alternative for the "gear" SF Symbol.
A single UI convention for toggle-state Toolbar Icons would be preferable, of course, but that's further complicated by the state when the Gear button is hidden… so would it instead make sense for Website settings to live within the Address Bar, just as Reload and soon Zoom will?
https://orionfeedback.org/d/563-show-current-zoom-level-in-address-bar-as-you-change-it
Perhaps that last point should be it's own suggestion…?