### 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) {
		for (int i = 0; i < 16; i++) {
			if (p_to_pos >= 0 && p_to_pos <= terrain_peering_bits[i]) {
				terrain_peering_bits[i] += 1;
			}
		}
	}
}
void TileData::move_terrain(int p_terrain_set, int p_from_index, int p_to_pos) {
	if (terrain_set == p_terrain_set) {
		for (int i = 0; i < 16; i++) {
			if (p_from_index == terrain_peering_bits[i]) {
				terrain_peering_bits[i] = (p_from_index < p_to_pos) ? p_to_pos - 1 : p_to_pos;
			} else {
				if (p_from_index < terrain_peering_bits[i]) {
					terrain_peering_bits[i] -= 1;
				}
				if (p_to_pos <= terrain_peering_bits[i]) {
					terrain_peering_bits[i] += 1;
				}
			}
		}
	}
}
void TileData::remove_terrain(int p_terrain_set, int p_index) {