### 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)
TERRAIN_MODE_MATCH_CORNERS_AND_SIDES = 0,
		TERRAIN_MODE_MATCH_CORNERS,
		TERRAIN_MODE_MATCH_SIDES,
	};
	enum TileShape {
		TILE_SHAPE_SQUARE,
		TILE_SHAPE_ISOMETRIC,
		TILE_SHAPE_HALF_OFFSET_SQUARE,
		TILE_SHAPE_HEXAGON,
	};
	enum TileLayout {
		TILE_LAYOUT_STACKED,
		TILE_LAYOUT_STACKED_OFFSET,
		TILE_LAYOUT_STAIRS_RIGHT,
		TILE_LAYOUT_STAIRS_DOWN,
		TILE_LAYOUT_DIAMOND_RIGHT,
		TILE_LAYOUT_DIAMOND_DOWN,
	};
	enum TileOffsetAxis {