By notifications I mean the light-blue messages for example about background processes that sometimes pop up on the top and stay there for a couple of seconds. Might be called something else. The problem is that many buttons are also on top (for example going one directory up or down in the file browser), so you can not use those buttons until the notification goes away by itself.
There should be a better solution? Ideally, the whole window shrinks a bit as long as the notification is there, but I understand this is difficult to implement. Or maybe put the notification on the bottom or the side? Or put a small X-button on the notification that closes them?