After much nixpkgs bisecting, I’ve determined that this started occurring when the GNOME: 47 → 48 PR was merged.
I haven’t yet been able to bisect which exact commit/package though because the PR was merged without squashing and most (all?) of the intermediate commits fail to build my system due to compilation errors with glib/gtk etc.
I’m very suspicious of this commit to gnome-settings-daemon, though: keyboard: Do not load xkb-options from localed when explicitly set to empty (3a9fce09) · Commits · GNOME / gnome-settings-daemon · GitLab . I notice that my dconf setting for /org/gnome/desktop/input-sources/xkb-options is populating to an empty list:
$ dconf read /org/gnome/desktop/input-sources/xkb-options
@as []
and that commit will make it stop getting written to.