### 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)
ERR_FAIL_COND_MSG(!allow_transform && p_flip_h, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	flip_h = p_flip_h;
	emit_signal(SNAME("changed"));
}
bool TileData::get_flip_h() const {
	return flip_h;
}
void TileData::set_flip_v(bool p_flip_v) {
	ERR_FAIL_COND_MSG(!allow_transform && p_flip_v, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	flip_v = p_flip_v;
	emit_signal(SNAME("changed"));
}
bool TileData::get_flip_v() const {
	return flip_v;
}
void TileData::set_transpose(bool p_transpose) {
	ERR_FAIL_COND_MSG(!allow_transform && p_transpose, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	transpose = p_transpose;
	emit_signal(SNAME("changed"));
}
bool TileData::get_transpose() const {