I am running the latest KDE neon User Edition with all the latest updates: DISTRIB_ID=neon DISTRIB_RELEASE=22.04 DISTRIB_CODENAME=jammy DISTRIB_DESCRIPTION="KDE neon 6.0" The system is configured to use Breeze Dark. After the update to Plasma 6.0.0, Gtk, and Electron applications installed from Flatpak, like Inkscape, Slack, and Audacity have been rendered in the light Breeze theme with icons from Breeze Dark. I can manually switch the theme in Inkscape to Dark, and it will render correctly, but if I leave the system default theme, it will be rendered as Breeze light with Breeze Dark icons, as described above. I also have Google Chrome installed from a .deb package and configured to use the GTK theme - it is rendered correctly in Breeze Dark.
A workaround is to run the following command: sudo flatpak override --env=GTK_THEME=Breeze Which actually gives weird results because, for example, in Inkscape's Preferences the system default theme is displayed as Breeze-Dark both before the override and after. But before the override, the UI is rendered in light colours, while after it, it is rendered in dark colours.
Update to the above comment: unfortunately, the workaround doesn't affect Slack (which is an Electron application).
I can confirm this issue: a.) After updating to Plasma 6.0, GTK 3 Flatpak apps do not use Breeze-GTK anymore. b.) When setting `GTK_THEME=Breeze` for all Flatpak apps, GTK 4 apps now render with a semi-broken light theme. My recommended workaround would be to only set the `GTK_THEME=Breeze` override for GTK 3 apps, as GTK 4 apps cannot be themed by KDE anyway. This can be done using an application like Flatseal. Something does indeed seem to be wrong here though.