I see… ok, nothing to do with native app support from Sync3 then.
For a 2016 you should have to change the HUB for a CP compatible one, check this thread for reference → Media Hub, CarPlay Compatible - 2015-2020 Ford/Lincoln - SYNC 3
Out of curiosity, did you ever see a “USB HUBs not supported” message while running your current system with 3.4 ?
Also, do you have an Android phone to test with?, Android is more forgiving that iOS…