Short answer no, you’ll need to create layers. otherwise how would the export convey that one tile is actually multiple tiles. If you find yourself needing a ton of layers for this, why not make the tree it’s own image that can go on an object layer? Objects can overlap with no issue.
another option is to create a looping tree tileset Zelda: A Link to the Past does this, allowing them to have a repeating canopy pattern rather than a bunch of tree layers, but this can be difficult with certain art style, and the amount of variety you desire
