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    "Since these phones running custom OS don’t fully adhere to security
    practices, Microsoft will issue an update to block and phase out such
    devices in a planned manner."
This statement by the article's author seems built out of poorly researched assumptions - like that stock OS all full adhere to security practices.
I have already cracked down on MS Authenticator --- I wrote my own --- and it's not very difficult to do.
For basic 6-digit codes sure. But MS authenticator uses push notice based approvals for many corporate SSO accounts including mine.
"push notice based approvals"

My simple work aound --- put the code in the clipboard. Use Ctrl-V to paste.

My authenticator app can also be configured to automatically launch a sign-in page.

You hardly ever have to use that system - despite the way they present it during enrollment (like zoom tries to get you to install their electron app every time you video conference).