Baseball organizations are so huge that you just can't look at specific players like Urshela and get any information from their path about an organization's competencies. A good org will have developmental failures and a bad org will have successes - you need to look at the total picture.
Toronto is clearly on the right path, as you say. You can also point to players like Kirk, Pearson, Hatch, Kay, Borucki, Font, Thornton, Groshans, etc. In one way or another guys like that are success stories.
You need to balance out all the stories and see which side is heavier and recognize that the majority of players will fail no matter what the org does. On the bad side Toronto hasn't had success with SRF, Alford, Drury, McKinney, Hector Perez, maybe Kevin Smith, to name a few.