I managed to properly fix that. As suggested in multiple threads related to this issue, package com.android.systemui holds this preference. Solution is to clear its data, but apparently it is disabled in the actual settings UI. However, it is still possible to do that by using ADB command
pm clear com.android.systemui
Obviously it will reset multiple user interface settings, but the good thing is the lack of popup really is fixable without root or full factory reset.
