### 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 (components.size() < 2) {
			return false;
		}
		String what = components[1];
		if (what == "name") {
			ctd->name = p_value;
		} else if (what == "texture") {
			ctd->texture = p_value;
		} else if (what == "tex_offset") {
			ctd->tex_offset = p_value;
		} else if (what == "material") {
			ctd->material = p_value;
		} else if (what == "modulate") {
			ctd->modulate = p_value;
		} else if (what == "region") {
			ctd->region = p_value;
		} else if (what == "tile_mode") {
			ctd->tile_mode = p_value;
		} else if (what.left(9) == "autotile") {
			what = what.substr(9);
			if (what == "bitmask_mode") {
				ctd->autotile_bitmask_mode = p_value;
			} else if (what == "icon_coordinate") {
				ctd->autotile_icon_coordinate = p_value;
			} else if (what == "tile_size") {
				ctd->autotile_tile_size = p_value;
			} else if (what == "spacing") {
				ctd->autotile_spacing = p_value;
			} else if (what == "bitmask_flags") {
				if (p_value.is_array()) {