### 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_COND(p_terrain < -1);
	terrain = p_terrain;
}
int TileSet::TerrainsPattern::get_terrain() const {
	return terrain;
}
void TileSet::TerrainsPattern::set_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit, int p_terrain) {
	ERR_FAIL_COND(p_peering_bit == TileSet::CELL_NEIGHBOR_MAX);
	ERR_FAIL_COND(!is_valid_bit[p_peering_bit]);
	ERR_FAIL_COND(p_terrain < -1);
	
	if (p_terrain >= 0 && bits[p_peering_bit] < 0) {
		not_empty_terrains_count++;
	} else if (p_terrain < 0 && bits[p_peering_bit] >= 0) {
		not_empty_terrains_count--;
	}
	bits[p_peering_bit] = p_terrain;
}
int TileSet::TerrainsPattern::get_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const {