It is possible for the visuals of a tile to overlap with other cells, I have done that a few times in some of my prototypes, by aligning the sprite in such a way the bottom square is the actual tile. So it means the tile is still square but when it gets drawn it will overlap what's behind, and when assembled they just line up nicely (i.e grass is taller, while the cell is just the ground part ; walls, where the cell is the bottom half).
However there is no way for one tile to occupy multiple cells at once. For these you'd need to use actual nodes because it goes outside the scope of what
TileMap was made for, and trying to support that anyways would be a lot of work to pull, in addition to everything else this node supports (sprites, collisions, navigation, autotiles, bucket fill, lines, selection, Y-Sort, isometric grids, custom grids, occluders, chunks...).
Maybe that could be done if we could define some tiles as being "compounds" of other tiles (which you'd still need to define), and placed like "stamps" just as a shortcut to "placing them all one by one", but in any case it either needs plugin work or a feature proposal.