### 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 (has_source(a[0]) && get_source(a[0])->has_tile(a[1]) && get_source(a[0])->has_alternative_tile(a[1], a[2])) {
			alternative_to_remove.push_back(a);
		}
	}
	for (int i = 0; i < alternative_to_remove.size(); i++) {
		Array a = alternative_to_remove[i];
		remove_alternative_level_tile_proxy(a[0], a[1], a[2]);
	}
}
void TileSet::clear_tile_proxies() {
	source_level_proxies.clear();
	coords_level_proxies.clear();
	alternative_level_proxies.clear();
	emit_changed();
}
int TileSet::add_pattern(Ref<TileMapPattern> p_pattern, int p_index) {
	ERR_FAIL_COND_V(!p_pattern.is_valid(), -1);
	ERR_FAIL_COND_V_MSG(p_pattern->is_empty(), -1, "Cannot add an empty pattern to the TileSet.");
	for (const Ref<TileMapPattern> &pattern : patterns) {
		ERR_FAIL_COND_V_MSG(pattern == p_pattern, -1, "TileSet has already this pattern.");
	}
	ERR_FAIL_COND_V(p_index > (int)patterns.size(), -1);
	if (p_index < 0) {
		p_index = patterns.size();
	}
	patterns.insert(p_index, p_pattern);
	emit_changed();
	return p_index;
}
Ref<TileMapPattern> TileSet::get_pattern(int p_index) {