@herf
Sorry for reopening this and I am not even sure there is anything you could do on your end.
With the registry flag it does indeed change the Windows theme as well, at least according to the setting ("Personalise" - "Colors" - "Chose your mode") Flux changes it completely to 'light' and 'dark' respectively, but the issue is that the setting is not actually applied for the Windows part, only for the app part.
Hope this makes sense. I.e. the apps are correctly changing colors automatically, but things like the Windows task bar will still display the earlier setting, even though the setting value is changed in Windows.
I understand that this is likely some type of Windows bug in how it manages the transition and not something you could fix on your end, but still thought I mention it to have it at least documented.