### 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)
if (tile_data->get_flip_v() ^ bool(p_alternative_tile & TileSetAtlasSource::TRANSFORM_FLIP_V)) {
			dest_rect.size.y = -dest_rect.size.y;
		}
		
		if (p_frame >= 0) {
			Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, p_frame);
			tex->draw_rect_region(p_canvas_item, dest_rect, source_rect, modulate, transpose, p_tile_set->is_uv_clipping());
		} else if (atlas_source->get_tile_animation_frames_count(p_atlas_coords) == 1) {
			Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, 0);
			tex->draw_rect_region(p_canvas_item, dest_rect, source_rect, modulate, transpose, p_tile_set->is_uv_clipping());
		} else {
			real_t speed = atlas_source->get_tile_animation_speed(p_atlas_coords);
			real_t animation_duration = atlas_source->get_tile_animation_total_duration(p_atlas_coords) / speed;
			
			
			real_t time_unscaled = 0.0;
			for (int frame = 0; frame < atlas_source->get_tile_animation_frames_count(p_atlas_coords); frame++) {
				real_t frame_duration_unscaled = atlas_source->get_tile_animation_frame_duration(p_atlas_coords, frame);
				real_t slice_start = time_unscaled / speed;
				real_t slice_end = (time_unscaled + frame_duration_unscaled) / speed;
				RenderingServer::get_singleton()->canvas_item_add_animation_slice(p_canvas_item, animation_duration, slice_start, slice_end, p_animation_offset);
				Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, frame);
				tex->draw_rect_region(p_canvas_item, dest_rect, source_rect, modulate, transpose, p_tile_set->is_uv_clipping());
				time_unscaled += frame_duration_unscaled;
			}
			RenderingServer::get_singleton()->canvas_item_add_animation_slice(p_canvas_item, 1.0, 0.0, 1.0, 0.0);
		}
	}
}
int TileMap::get_layers_count() const {