Here's some OTRS user feedback on how it should work with the system theme:

1. The functionality to "follow the system theme" should be orthogonal to the actual concrete color themes (light, sepia, gray, black), as opposed to the current implementation which introduces a mutually exclusive "theme" that represents the system's theme. The purpose being that you should not lose your preference to follow the system theme even if you need to temporarily override the app's color theme for some reason (quick switching is why the themes are in an easily accessible popover, after all). The simplest way is to just make this preference a standard iOS switch. Yes, this switch will sometimes appear to be "out of sync" with the actual concrete theme of the app, but that's inconsequential since this option only represents the user's desire to switch the app theme when the system theme changes — not the desire for any particular theme at all points in time. It also only happens if the user explicitly overrides the selected color theme, and will be "in sync" again the next time the system theme changes. Additionally, as a result of the "follow system theme" option becoming independent and no longer getting overwritten by manually changing color themes in the theme selection popover, it can now become a set-and-forget option that can reside solely in the app's settings view if, for some reason, you'd prefer not to place this option in the popover.

2. Whenever a user selects one of the two dark themes (black, gray) they are implicitly indicating their preferred dark theme, and the same thing for the two light themes. In other words, just use the last used light and dark theme respectively, and there will be no need to introduce any new UI controls for configuring "preferred light/dark themes" (a good thing).