### 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)
GDCLASS(DebugQuadrant, RefCounted);
public:
	Vector2i quadrant_coords;
	SelfList<CellData>::List cells;
	RID canvas_item;
	SelfList<DebugQuadrant> dirty_quadrant_list_element;
	
	DebugQuadrant(const DebugQuadrant &p_other) :
			dirty_quadrant_list_element(this) {
		quadrant_coords = p_other.quadrant_coords;
		cells = p_other.cells;
		canvas_item = p_other.canvas_item;
	}
	DebugQuadrant() :
			dirty_quadrant_list_element(this) {
	}
	~DebugQuadrant() {
		cells.clear();
	}
};
#endif 
class RenderingQuadrant : public RefCounted {
	GDCLASS(RenderingQuadrant, RefCounted);
public:
	struct CoordsWorldComparator {
		_ALWAYS_INLINE_ bool operator()(const Vector2 &p_a, const Vector2 &p_b) const {