### 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)

v.y = val.y;
						priority = (int)val.z;
						ctd->autotile_priority_map.insert(v, priority);
					}
					p.pop_front();
				}
			} else if (what == "z_index_map") {
				Array p = p_value;
				Vector3 val;
				Vector2 v;
				int z_index;
				while (p.size() > 0) {
					val = p[0];
					if (val.z != 0) {
						v.x = val.x;
						v.y = val.y;
						z_index = (int)val.z;
						ctd->autotile_z_index_map.insert(v, z_index);
					}
					p.pop_front();
				}
			}
		} else if (what == "shapes") {
			Array p = p_value;
			for (int i = 0; i < p.size(); i++) {
				CompatibilityShapeData csd;
				Dictionary d = p[i];
				for (int j = 0; j < d.size(); j++) {
					String key = d.get_key_at_index(j);
					if (key == "autotile_coord") {