This is another NES Inconsistency.
In a dungeon, when Link steps on a warp tile that goes to the Item Cellar or Passageway, he has to disappear immediately before the screen fades out and appear in Item Cellar or Passageway after the screen fades in. Same way for exiting the Item Cellar or Passageway to the dungeon room.
This bug is persistent. Maybe that's why Link appears on the top screen edge when the dungeon room screen fades in before he moves to the warp return point (with freeform dungeons rule checked).
EDIT: This is my 10th post so far.