Hi Christoph,
I'm closing this bug: what you saw was intended upstream behaviour, and
the feature involved no longer exists.
Since Cinnamon 3.8 (2018) the "Window borders" list only offers themes
that ship metacity-1/metacity-theme-3.xml, because older metacity-1 and
metacity-2 themes don't draw their borders correctly. TraditionalOk from
mate-themes only ships metacity-theme-1.xml, and no Debian package ships
/usr/share/themes/Default/metacity-1 at all, so neither could appear in
the list; the chooser still displays the currently selected theme even
when it is filtered out, which is exactly what you observed after
setting the dconf key by hand. Removing packages was not the cause: your
theme had been selectable before the filter was introduced, and the
setting simply survived the upgrades.
Upstream then dropped the setting altogether: the chooser was removed
from the UI in Cinnamon 5.4.2 and the leftover code in 5.6.4, and
current muffin no longer reads org.cinnamon.desktop.wm.preferences/theme
at all — window decorations now follow the GTK theme. Unstable currently
ships cinnamon 6.6.9, where the "Window borders" page is gone.
Thanks for the report, and sorry for the very long silence.