FlatpakPermissionModel: Update "settings changed" state when saving non-default entries
Entries which are not enabled by default don't have any meaningful default value in upstream metadata, but we reuse the field to represent currently persisted value in user's overrides file. It saves us from slightly larger refactoring in which logical expressions of the SettingHighlighter would need to be rewritten with valueType and (currently unexposed) OverrideValue role in mind. (cherry picked from commit aa9bfc8d)
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