That's OK. I THINK I have it solved but won't know for a while for sure. If you go to Settings -> System -> Focus Alert you turn off everything and check the box at the bottom telling it to let you know what you missed. The rest of the setting are actually to automatically turn on Focus Assist under specific situations Which it does even though Focus Assist is already on. It is this automatically turning on that causes the annoying alert that Focus Alert has been turned on.
While Focus Alert will not throw up a message for most things I DO have it set to still put through system alarms. In case some don't know the purpose of Focus Alert it will stop popup alerts when a screen is duplicated, an app is in full screen mode or playing a game.
Fingers crossed!