How to know the doneness for a tough cut of meat
There are two basic cooking methods for tough cuts:


Cook for a long time ("low and slow"): this is appropriate for large pieces like roasts
Sear very quickly on both sides and remove while barely medium-rare: this is appropriate for thin steaks


The thing is, while many people mention the second method, it's still going to produce a relatively tough piece of meat.  Some people claim that you could take a piece of chuck steak or round steak and make it as tender as a ribeye as long as you cook it fast and don't overcook it.  That's just not true, but it's a way of cooking the meat fast, while minimizing the amount of toughness that occurs with fast cooking.

Usually you'd want to do this either with very thin steaks (which is one the reasons flank is often sliced very thin) or with the type of meat that you'd slice into thin strips before serving.  Many people cook a traditional "London Broil" this way (which tends to be a relatively lean and somewhat tough cut): very fast cooking on both sides, then slice thinly and serve.

The reason for these two conflicting pieces of advice is that "tough" meat reaches its maximum toughness when it's just "well-done."  You generally want to cook it to medium-rare, because that's when beef is juiciest, so you get juice and still less tough.  But once you go beyond medium-rare, it just gets tougher and less juicy.  At that point, the way forward is to continue to cook for a long time, which will eventually break down the tissues that make the meat tough (as you note), so you'll end up with thoroughly cooked but more tender meat in the end.