It's annoying for end-users (and you), but why not display a window with a SUPERSHORT message explaining that MacBooks with a notch might hide the icon on the first launch? Have a button or link to explain more for people who want it.
Shouldn't have to, but it might mitigate some of the stuff a FAQ won't catch.
I forgot such messages directly. Then when It realize I saw an important message tens seconds ago I have no way of going back. I can not press undo and get that message again.
Error messages are a bad design. Error logs are ok. Global undo would be king like the undo close tab feature in browsers.