If you enable extensions while settings is open, pref will not contain extension-controlled information.

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Triage info from dbeam@:

In the case of extension-controlled prefs, extensions like fillr use

  chrome.privacy.services.autofillEnabled.set({value: false});

To disable Chrome's native Autofill.

When this happens, code runs[1] in chrome to set a pref in the:

1) profile pref store
2) extensions pref store

We observe changes to the profile pref store.  So the order is:

1) set value in profile pref store
-> change happens
2) set value in extensions pref store

Unfortunately, we ask in the observer whether
pref->IsExtensionControlled()[2], which check which store the value comes from.

This will change on the next line of code, but isn't updated yet.