### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

ret += Vector2i(1, 0);
					}
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
					ret = Vector2(ret.x + ret.y / 2, ret.y / 2 - ret.x).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, 0);
					} else if (in_top_right_triangle) {
						ret += Vector2i(0, -1);
					}
					break;
			}
		} else { 
			
			Vector2 raw_pos = ret;
			if (Math::posmod(Math::floor(ret.x), 2) ^ (tile_layout == TileSet::TILE_LAYOUT_STACKED_OFFSET)) {
				ret = Vector2(Math::floor(ret.x), Math::floor(ret.y + 0.5) - 0.5);
			} else {
				ret = ret.floor();
			}
			
			Vector2 in_tile_pos = raw_pos - ret;
			bool in_top_left_triangle = (in_tile_pos - Vector2(0.0, 0.5)).cross(Vector2(1.0 / overlapping_ratio - 1, -0.5)) > 0;
			bool in_bottom_left_triangle = (in_tile_pos - Vector2(0.0, 0.5)).cross(Vector2(1.0 / overlapping_ratio - 1, 0.5)) <= 0;
			switch (tile_layout) {
				case TileSet::TILE_LAYOUT_STACKED:
					ret = ret.floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, Math::posmod(Math::floor(ret.x), 2) ? 0 : -1);
					} else if (in_bottom_left_triangle) {