### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
} else if (p_cell_neighbor == TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE) {
							return p_coords + Vector2i(0, 1);
						} else {
							ERR_FAIL_V(p_coords);
						}
					}
				} else {
					if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
						if ((shape == TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_RIGHT_CORNER) ||
								(shape != TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_RIGHT_SIDE)) {
							return p_coords + Vector2i(1, -1);
						} else if (p_cell_neighbor == TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE) {
							return p_coords + Vector2i(1, 0);
						} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_BOTTOM_CORNER) {
							return p_coords + Vector2i(1, 1);
						} else if (p_cell_neighbor == TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE) {
							return p_coords + Vector2i(0, 1);
						} else if ((shape == TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_LEFT_CORNER) ||
								(shape != TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_LEFT_SIDE)) {
							return p_coords + Vector2i(-1, 1);
						} else if (p_cell_neighbor == TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE) {
							return p_coords + Vector2i(-1, 0);
						} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC && p_cell_neighbor == TileSet::CELL_NEIGHBOR_TOP_CORNER) {
							return p_coords + Vector2i(-1, -1);
						} else if (p_cell_neighbor == TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE) {
							return p_coords + Vector2i(0, -1);
						} else {
							ERR_FAIL_V(p_coords);
						}
					} else {