Andrew,
I am not sure where you're getting the information about Modern Authentication breaking APM-as-ADFS-proxy deployment, but I think there may be some confusion going on around this change.
Modern Authentication mode, aka ADAL, are leverage web browser for authentication of thick clients, and such mode of authentication is fully compatible with APM. If anything, support for Modern Authentication brings out additional opportunities for F5 customers who are using APM because they are free to leverage a multitude of MFA options to secure access to Office 365 and potentially simplify their federation configuration by having APM federate users to Office 365 instead of ADFS.
To get an idea of what new possibilities Modern Authentication brings, check out this video that I recorded about securing access to Officee 365 from the full Outlook client leveraging MFA. https://www.youtube.com/watch?v=s5W6cgrxyrY