### 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)

ERR_FAIL_COND_MSG(p_coords.x < 0 || p_coords.y < 0, vformat("Cannot set cell with negative coords in a TileMapPattern. Wrong coords: %s", p_coords));
	size = size.max(p_coords + Vector2i(1, 1));
	pattern[p_coords] = TileMapCell(p_source_id, p_atlas_coords, p_alternative_tile);
	emit_changed();
}
bool TileMapPattern::has_cell(const Vector2i &p_coords) const {
	return pattern.has(p_coords);
}
void TileMapPattern::remove_cell(const Vector2i &p_coords, bool p_update_size) {
	ERR_FAIL_COND(!pattern.has(p_coords));
	pattern.erase(p_coords);
	if (p_update_size) {
		size = Size2i();
		for (const KeyValue<Vector2i, TileMapCell> &E : pattern) {
			size = size.max(E.key + Vector2i(1, 1));
		}
	}
	emit_changed();
}
int TileMapPattern::get_cell_source_id(const Vector2i &p_coords) const {