### 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(!allow_transform && p_flip_h, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	flip_h = p_flip_h;
	emit_signal(SNAME("changed"));
}
bool TileData::get_flip_h() const {
	return flip_h;
}
void TileData::set_flip_v(bool p_flip_v) {
	ERR_FAIL_COND_MSG(!allow_transform && p_flip_v, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	flip_v = p_flip_v;
	emit_signal(SNAME("changed"));
}
bool TileData::get_flip_v() const {
	return flip_v;
}
void TileData::set_transpose(bool p_transpose) {
	ERR_FAIL_COND_MSG(!allow_transform && p_transpose, "Transform is only allowed for alternative tiles (with its alternative_id != 0)");
	transpose = p_transpose;
	emit_signal(SNAME("changed"));
}
bool TileData::get_transpose() const {