The last hidden/various settings:
show_symbol_list_expanders, use_gtk_word_boundaries - Both are safe to change, affect the newly opened files and require restart for the already open files.
Summary:
6 prefs require restart.
Another 6 (including allow_always_save) currently require restart, but that can be easily fixed by calling a function or two when updating the preferences.
All prefs are safe to change, except for allow_always_save. I think that enabling Save all on allow_always_save = true even if no files are modified is a mistake. In such a case, Save all does nothing - in particular, it does not save all files regardless of the modification flag - so having it enabled makes no sense and can be misleading.
If you agree on that, I'll make the changes required for the six prefs that can be applied without restarting, and include them in the next version of the various prefs diff.