### 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("get_layer_y_sort_origin", "layer"), &TileMap::get_layer_y_sort_origin);
	ClassDB::bind_method(D_METHOD("set_layer_z_index", "layer", "z_index"), &TileMap::set_layer_z_index);
	ClassDB::bind_method(D_METHOD("get_layer_z_index", "layer"), &TileMap::get_layer_z_index);
	ClassDB::bind_method(D_METHOD("set_layer_navigation_enabled", "layer", "enabled"), &TileMap::set_layer_navigation_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_navigation_enabled", "layer"), &TileMap::is_layer_navigation_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_navigation_map", "layer", "map"), &TileMap::set_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("get_layer_navigation_map", "layer"), &TileMap::get_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("set_collision_animatable", "enabled"), &TileMap::set_collision_animatable);
	ClassDB::bind_method(D_METHOD("is_collision_animatable"), &TileMap::is_collision_animatable);
	ClassDB::bind_method(D_METHOD("set_collision_visibility_mode", "collision_visibility_mode"), &TileMap::set_collision_visibility_mode);
	ClassDB::bind_method(D_METHOD("get_collision_visibility_mode"), &TileMap::get_collision_visibility_mode);
	ClassDB::bind_method(D_METHOD("set_navigation_visibility_mode", "navigation_visibility_mode"), &TileMap::set_navigation_visibility_mode);
	ClassDB::bind_method(D_METHOD("get_navigation_visibility_mode"), &TileMap::get_navigation_visibility_mode);
	ClassDB::bind_method(D_METHOD("set_cell", "layer", "coords", "source_id", "atlas_coords", "alternative_tile"), &TileMap::set_cell, DEFVAL(TileSet::INVALID_SOURCE), DEFVAL(TileSetSource::INVALID_ATLAS_COORDS), DEFVAL(0));
	ClassDB::bind_method(D_METHOD("erase_cell", "layer", "coords"), &TileMap::erase_cell);
	ClassDB::bind_method(D_METHOD("get_cell_source_id", "layer", "coords", "use_proxies"), &TileMap::get_cell_source_id, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_atlas_coords", "layer", "coords", "use_proxies"), &TileMap::get_cell_atlas_coords, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_alternative_tile", "layer", "coords", "use_proxies"), &TileMap::get_cell_alternative_tile, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_tile_data", "layer", "coords", "use_proxies"), &TileMap::get_cell_tile_data, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_coords_for_body_rid", "body"), &TileMap::get_coords_for_body_rid);
	ClassDB::bind_method(D_METHOD("get_layer_for_body_rid", "body"), &TileMap::get_layer_for_body_rid);
	ClassDB::bind_method(D_METHOD("get_pattern", "layer", "coords_array"), &TileMap::get_pattern);
	ClassDB::bind_method(D_METHOD("map_pattern", "position_in_tilemap", "coords_in_pattern", "pattern"), &TileMap::map_pattern);
	ClassDB::bind_method(D_METHOD("set_pattern", "layer", "position", "pattern"), &TileMap::set_pattern);
	ClassDB::bind_method(D_METHOD("set_cells_terrain_connect", "layer", "cells", "terrain_set", "terrain", "ignore_empty_terrains"), &TileMap::set_cells_terrain_connect, DEFVAL(true));
	ClassDB::bind_method(D_METHOD("set_cells_terrain_path", "layer", "path", "terrain_set", "terrain", "ignore_empty_terrains"), &TileMap::set_cells_terrain_path, DEFVAL(true));
	ClassDB::bind_method(D_METHOD("fix_invalid_tiles"), &TileMap::fix_invalid_tiles);
	ClassDB::bind_method(D_METHOD("clear_layer", "layer"), &TileMap::clear_layer);
	ClassDB::bind_method(D_METHOD("clear"), &TileMap::clear);
	ClassDB::bind_method(D_METHOD("update_internals"), &TileMap::update_internals);