I hope they'll include a "Stop the nanny" flag in chrome://flags as well. I mean you can't even change the new tab page to a custom .html, without Chrome nagging you at every launch if the settings are correct. If you make a manifest.json and load as an unpacked extension, it will moan about that. FFS, I know what you're trying to do with Joe/Jane Noob, but at least give me something to skip that if I know what I'm d…
The hard part here is that, wherever you'd decide to persist a "don't bug me any more about this" flag, malware could also potentially write that same flag to that same place. For example, Windows UAC is frequently set to the "don't bug me about this, just auto-elevate" setting by malware.
Build a new binary - offer users to install a "developer" build of Chrome which is exactly the same as the mainstream "release" build, except it allows disabling the protections.