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