### 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)
ClassDB::bind_method(D_METHOD("remove_coords_level_tile_proxy", "source_from", "coords_from"), &TileSet::remove_coords_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("set_alternative_level_tile_proxy", "source_from", "coords_from", "alternative_from", "source_to", "coords_to", "alternative_to"), &TileSet::set_alternative_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("get_alternative_level_tile_proxy", "source_from", "coords_from", "alternative_from"), &TileSet::get_alternative_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("has_alternative_level_tile_proxy", "source_from", "coords_from", "alternative_from"), &TileSet::has_alternative_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("remove_alternative_level_tile_proxy", "source_from", "coords_from", "alternative_from"), &TileSet::remove_alternative_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("map_tile_proxy", "source_from", "coords_from", "alternative_from"), &TileSet::map_tile_proxy);
	ClassDB::bind_method(D_METHOD("cleanup_invalid_tile_proxies"), &TileSet::cleanup_invalid_tile_proxies);
	ClassDB::bind_method(D_METHOD("clear_tile_proxies"), &TileSet::clear_tile_proxies);
	
	ClassDB::bind_method(D_METHOD("add_pattern", "pattern", "index"), &TileSet::add_pattern, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("get_pattern", "index"), &TileSet::get_pattern, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("remove_pattern", "index"), &TileSet::remove_pattern);
	ClassDB::bind_method(D_METHOD("get_patterns_count"), &TileSet::get_patterns_count);
	ADD_GROUP("Rendering", "");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "uv_clipping"), "set_uv_clipping", "is_uv_clipping");
	ADD_ARRAY("occlusion_layers", "occlusion_layer_");
	ADD_GROUP("", "");
	ADD_ARRAY("physics_layers", "physics_layer_");
	ADD_ARRAY("terrain_sets", "terrain_set_");
	ADD_ARRAY("navigation_layers", "navigation_layer_");
	ADD_ARRAY("custom_data_layers", "custom_data_layer_");
	
	BIND_ENUM_CONSTANT(TILE_SHAPE_SQUARE);
	BIND_ENUM_CONSTANT(TILE_SHAPE_ISOMETRIC);
	BIND_ENUM_CONSTANT(TILE_SHAPE_HALF_OFFSET_SQUARE);
	BIND_ENUM_CONSTANT(TILE_SHAPE_HEXAGON);
	BIND_ENUM_CONSTANT(TILE_LAYOUT_STACKED);
	BIND_ENUM_CONSTANT(TILE_LAYOUT_STACKED_OFFSET);
	BIND_ENUM_CONSTANT(TILE_LAYOUT_STAIRS_RIGHT);
	BIND_ENUM_CONSTANT(TILE_LAYOUT_STAIRS_DOWN);