### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

ERR_FAIL_INDEX(p_from_index, occluders.size());
	ERR_FAIL_INDEX(p_to_pos, occluders.size() + 1);
	occluders.insert(p_to_pos, occluders[p_from_index]);
	occluders.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
}
void TileData::remove_occlusion_layer(int p_index) {
	ERR_FAIL_INDEX(p_index, occluders.size());
	occluders.remove_at(p_index);
}
void TileData::add_physics_layer(int p_to_pos) {
	if (p_to_pos < 0) {
		p_to_pos = physics.size();
	}
	ERR_FAIL_INDEX(p_to_pos, physics.size() + 1);
	physics.insert(p_to_pos, PhysicsLayerTileData());
}
void TileData::move_physics_layer(int p_from_index, int p_to_pos) {
	ERR_FAIL_INDEX(p_from_index, physics.size());
	ERR_FAIL_INDEX(p_to_pos, physics.size() + 1);
	physics.insert(p_to_pos, physics[p_from_index]);
	physics.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
}
void TileData::remove_physics_layer(int p_index) {
	ERR_FAIL_INDEX(p_index, physics.size());
	physics.remove_at(p_index);
}
void TileData::add_terrain_set(int p_to_pos) {