Disbale the 'Some settings have been reset' "feature"

Sometimes it happens that I open my browser and get greeted by the message that "some settings have been reset", with the reason that settings might have been changed outside of the browser. I understand that this is a security feature, however this "feature" regularly resets all my settings. Having to reconfigure my entire browser, find a list of all extensions I had installed and reinstalling them and reconfiguring them is utterly irritating. Chromium resetting everything has happened on following occasions:

• Changing browser flags
• Updating registry values for app compatibility mode, for applications that are not related to chromium in any way
• Uninstalling TerraCopy
• Changing attributes of a folder inside the chromium data directory (%localappdata%\chromium\User Data)

Is there any way to disable this intrusive behaviour, either by policies or by some other way?

I'm so fed up.