### 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)
Size2 size = get_tile_texture_region(p_atlas_coords).size;
	Rect2 rect = Rect2(-size / 2 - get_tile_data(p_atlas_coords, p_alternative_tile)->get_texture_origin(), size);
	return rect.has_point(p_position);
}
int TileSetAtlasSource::alternative_no_transform(int p_alternative_id) {
	return p_alternative_id & ~(TRANSFORM_FLIP_H | TRANSFORM_FLIP_V | TRANSFORM_TRANSPOSE);
}
Ref<Texture2D> TileSetAtlasSource::get_runtime_texture() const {
	if (use_texture_padding) {
		return padded_texture;
	} else {
		return texture;
	}
}
Rect2i TileSetAtlasSource::get_runtime_tile_texture_region(Vector2i p_atlas_coords, int p_frame) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), Rect2i(), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_INDEX_V(p_frame, (int)tiles[p_atlas_coords].animation_frames_durations.size(), Rect2i());
	Rect2i src_rect = get_tile_texture_region(p_atlas_coords, p_frame);
	if (use_texture_padding) {
		const TileAlternativesData &tad = tiles[p_atlas_coords];
		Vector2i frame_coords = p_atlas_coords + (tad.size_in_atlas + tad.animation_separation) * ((tad.animation_columns > 0) ? Vector2i(p_frame % tad.animation_columns, p_frame / tad.animation_columns) : Vector2i(p_frame, 0));
		Vector2i base_pos = frame_coords * (texture_region_size + Vector2i(2, 2)) + Vector2i(1, 1);
		return Rect2i(base_pos, src_rect.size);
	} else {
		return src_rect;
	}
}
void TileSetAtlasSource::move_tile_in_atlas(Vector2i p_atlas_coords, Vector2i p_new_atlas_coords, Vector2i p_new_size) {