Hi Simon,
sorry for the very long delay in answering.
The symptom you describe, the option still checked in the UI but not
actually applied after a reboot, came from the old keyboard stack, where
the setting was written through libgnomekbd and the cinnamon-control-
center region panel while a different component was responsible for
applying it at login.
That stack is gone. Upstream rewrote keyboard handling in Cinnamon 6.6.0
(commit 5fd574898, "Modernize keyboard handling"), which reached Debian
with cinnamon 6.6.7-1. XKB options now live in
org.cinnamon.desktop.input-sources xkb-options, they are configured from
the XKB Options page in cinnamon-settings, and Cinnamon itself applies
them at session startup and immediately on change;
cinnamon-settings-daemon only seeds the initial values from localed when
they are empty.
I'm therefore closing this bug. If the option is still not applied after
a reboot on trixie or sid, please open a new report including the output
of
gsettings get org.cinnamon.desktop.input-sources xkb-options
setxkbmap -query
taken right after logging in.
Thanks for the report,
Fabio