### 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)
ERR_FAIL_COND_V(p_margins.x < 0 || p_margins.y < 0, PackedVector2Array());
	ERR_FAIL_COND_V(p_separation.x < 0 || p_separation.y < 0, PackedVector2Array());
	ERR_FAIL_COND_V(p_texture_region_size.x <= 0 || p_texture_region_size.y <= 0, PackedVector2Array());
	
	Size2 new_grid_size;
	if (p_texture.is_valid()) {
		Size2i valid_area = p_texture->get_size() - p_margins;
		
		if (valid_area.x >= p_texture_region_size.x && valid_area.y >= p_texture_region_size.y) {
			valid_area -= p_texture_region_size;
			new_grid_size = Size2i(1, 1) + valid_area / (p_texture_region_size + p_separation);
		}
	}
	Vector<Vector2> output;
	for (KeyValue<Vector2i, TileAlternativesData> &E : tiles) {
		for (unsigned int frame = 0; frame < E.value.animation_frames_durations.size(); frame++) {
			Vector2i frame_coords = E.key + (E.value.size_in_atlas + E.value.animation_separation) * ((E.value.animation_columns > 0) ? Vector2i(frame % E.value.animation_columns, frame / E.value.animation_columns) : Vector2i(frame, 0));
			frame_coords += E.value.size_in_atlas;
			if (frame_coords.x > new_grid_size.x || frame_coords.y > new_grid_size.y) {
				output.push_back(E.key);
				break;
			}
		}
	}
	return output;
}
Rect2i TileSetAtlasSource::get_tile_texture_region(Vector2i p_atlas_coords, int p_frame) const {