Vlad Yes, looks like Safari indeed does it, but this is one of those cases where that should not hold us back. The hiding of top part of pop-ups makes it especially difficult to work with extensions. Also, this issue is just exacerbated with bookmarks bar turned on (Cmd+Shift+B).
Safari has less extensiosn support, so this issue might not show up often. Also, Safari has "Always Hide Toolbar in Full Screen" off by default, and I didn't even know it existed, so I never used it. Orion, otoh, has "Always Hide Toolbar in Full Screen" on by default, hence more users noticing it. Given this and the higher number of extensions on Orion, I can see this issue being a major hindrance if unresolved just cause "that's what Safari does"