I've just made a test: multiple accounts using the same account/email and there is no conflict.
I even have a matching icon of the issuer for each entry; the issuer is registered for each entry.
I am using the MS Authenticator for years and I've never had any problem of that sort, and of course, I am always using the same email as my account/username.
Anyway, I'm just putting the result of my test. It's not like this going to change your mind about the authenticator or Microsoft itself here...
I even have a matching icon of the issuer for each entry; the issuer is registered for each entry.
I am using the MS Authenticator for years and I've never had any problem of that sort, and of course, I am always using the same email as my account/username.
Anyway, I'm just putting the result of my test. It's not like this going to change your mind about the authenticator or Microsoft itself here...