I can not see this issue on meta, but on my instance, this is caused by this CSS code:
The code is there to add some margin between top buttons and the welcome banner, but it’s also enforcing the margin on places where it should not be, the margin also stays enabled even if the welcome banner is hidden, for example, because of staff or trust level.
EDIT: sloppy fix?
Remove the margin from this class:
Thanks for letting me know! There are some cases where the banner is immediately above another banner or alert, which is why it needs the margin. I was able to relocate the margin to remove the impact when the component is hidden.