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The latest versions of Office (Outlook, Skype for Bus, OneDrive for Bus) have support for MFA natively; either via token or the Microsoft Authenticator app (what I use). My guess is that the warning is because you can't use PowerShell to connect to O365 if you have MFA enabled; app passwords won't work with PowerShell either (we tried).
Very frustrating because those are the accounts you would most want MFA on. To my knowledge, MFA only works with the Azure PowerShell module, but you can't get to Exchange Online via that method so in most cases it's useless.
Doing some quick Googling just now to find the information we found earlier, I found a link to a supposed preview release of the Exchange Online PowerShell module that does support MFA (I have not tested it myself... yet).
Forum: https://techcommunity.microsoft.com/t5/Identity-Authentication/Authenticating-to-O365-using-Powershe...
Download: http://aka.ms/exopspreview
Using MFA for Office 365, users are required to acknowledge a phone call, text message, or app notification on their smart phones after A form of multi-factor authentication is included with Office 365, but you can also purchase Azure multi-factor authentication that includes extended functionality. Jan 11, 2017 Outlook 2016 for MAC - Issue with MFA when adding a second account Hello, I came across a very particular scenario where I have working Office 365 mailbox (hybrid with exchange 2016, mailbox was migrated) working on Outlook for mac.