### 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)

if (layer_index >= physics.size()) {
				if (tile_set) {
					return false;
				} else {
					physics.resize(layer_index + 1);
				}
			}
			if (components[1] == "linear_velocity") {
				set_constant_linear_velocity(layer_index, p_value);
				return true;
			} else if (components[1] == "angular_velocity") {
				set_constant_angular_velocity(layer_index, p_value);
				return true;
			} else if (components[1] == "polygons_count") {
				if (p_value.get_type() != Variant::INT) {
					return false;
				}
				set_collision_polygons_count(layer_index, p_value);
				return true;
			}
		} else if (components.size() == 3 && components[1].begins_with("polygon_") && components[1].trim_prefix("polygon_").is_valid_int()) {
			int polygon_index = components[1].trim_prefix("polygon_").to_int();
			ERR_FAIL_COND_V(polygon_index < 0, false);
			if (components[2] == "points" || components[2] == "one_way" || components[2] == "one_way_margin") {
				if (layer_index >= physics.size()) {
					if (tile_set) {
						return false;
					} else {
						physics.resize(layer_index + 1);
					}