Yes, this strikes me as something that should go into chrome://settings under the Accessibility section, for several reasons.
First, as you noted, flags are for temporary settings and debugging flags. While about:flags is a place to tinker, it's not intended for most users to find their way in there, whereas preferences are designed to help users find what they're looking for.
Second, in settings we have mechanisms to bounce people to system settings when the setting is maintained by the system. An example I can think of that was recently added was styling media captions; on the Mac and Windows it bounces the user to the system settings, and handles the setting for all other platforms. Even though your settings is intended to override the system setting, that may be useful to build your UI. (Maybe a link to access the system setting and a switch to force it off? The UI folks can help you craft something good here.)
Third, the flags page is, honestly, a UI mess. For good reason, though, since it helps discourage people from mucking around in there. The preferences pages are neatly organized into sections; there already is an Accessibility section where your setting would fit well.
Fourth, and importantly, about:flags is not localized. As a place for temporary settings and debugging flags, that's the decision we've made, but for a setting that an average user may need to access, sticking it in a place in Chrome's UI that is in a language they don't speak is not the right approach.
This belongs in the settings page. Yes, we try to minimize the number of switches (both settings and flags!) but if something needs to be set, it needs to be set. Talk to the settings people; they should be helpful.
Thank you for emailing us. If there's anything we can do to support you further with this setting, please let us know.
Avi