### 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 (terrain_set == p_terrain_set) {
		if (terrain == p_index) {
			terrain = -1;
		}
		for (int i = 0; i < 16; i++) {
			if (terrain_peering_bits[i] == p_index) {
				terrain_peering_bits[i] = -1;
			} else if (terrain_peering_bits[i] > p_index) {
				terrain_peering_bits[i] -= 1;
			}
		}
	}
}
void TileData::add_navigation_layer(int p_to_pos) {
	if (p_to_pos < 0) {
		p_to_pos = navigation.size();
	}
	ERR_FAIL_INDEX(p_to_pos, navigation.size() + 1);
	navigation.insert(p_to_pos, Ref<NavigationPolygon>());
}
void TileData::move_navigation_layer(int p_from_index, int p_to_pos) {