Hello,
The little box telling me that there is an "Update available for some of your boards and librairies" does stay in front of my screen, and this is quite unpleasant.
I join a screenshot of it.
Regards
See IDE should not steal focus for "Update available for some of your libraries" · Issue #3809 · arduino/Arduino · GitHub. It is marked Help Wanted so if anyone can fix it I'm sure the developers would be grateful.