### 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)
}
	}
	
	double overlapping_ratio = 1.0;
	if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.y *= overlapping_ratio;
	} else { 
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.x *= overlapping_ratio;
	}
	return (ret + Vector2(0.5, 0.5)) * tile_set->get_tile_size();
}
Vector2i TileMap::local_to_map(const Vector2 &p_local_position) const {
	ERR_FAIL_COND_V(!tile_set.is_valid(), Vector2i());
	Vector2 ret = p_local_position;
	ret /= tile_set->get_tile_size();
	TileSet::TileShape tile_shape = tile_set->get_tile_shape();
	TileSet::TileOffsetAxis tile_offset_axis = tile_set->get_tile_offset_axis();
	TileSet::TileLayout tile_layout = tile_set->get_tile_layout();
	
	double overlapping_ratio = 1.0;