### 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_terrain_set, terrain_sets.size());
	ERR_FAIL_INDEX(p_terrain_index, terrain_sets[p_terrain_set].terrains.size());
	terrain_sets.write[p_terrain_set].terrains.write[p_terrain_index].name = p_name;
	emit_changed();
}
String TileSet::get_terrain_name(int p_terrain_set, int p_terrain_index) const {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), String());
	ERR_FAIL_INDEX_V(p_terrain_index, terrain_sets[p_terrain_set].terrains.size(), String());
	return terrain_sets[p_terrain_set].terrains[p_terrain_index].name;
}
void TileSet::set_terrain_color(int p_terrain_set, int p_terrain_index, Color p_color) {
	ERR_FAIL_INDEX(p_terrain_set, terrain_sets.size());
	ERR_FAIL_INDEX(p_terrain_index, terrain_sets[p_terrain_set].terrains.size());
	if (p_color.a != 1.0) {
		WARN_PRINT("Terrain color should have alpha == 1.0");
		p_color.a = 1.0;
	}
	terrain_sets.write[p_terrain_set].terrains.write[p_terrain_index].color = p_color;
	emit_changed();
}
Color TileSet::get_terrain_color(int p_terrain_set, int p_terrain_index) const {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), Color());
	ERR_FAIL_INDEX_V(p_terrain_index, terrain_sets[p_terrain_set].terrains.size(), Color());
	return terrain_sets[p_terrain_set].terrains[p_terrain_index].color;
}
bool TileSet::is_valid_terrain_peering_bit_for_mode(TileSet::TerrainMode p_terrain_mode, TileSet::CellNeighbor p_peering_bit) const {