"When you go into a 5-man instance, you expect to clear it, even if it is your first time going to that instance. You may wipe once or twice, but the general expectation is that you will finish that instance. In this case, an instance time limit is a good idea. If you hit the trash respawn, it's a sign that something is wrong, and perhaps it might be a better idea to try again later, maybe with a different group or after gearing up a bit more.
... In contrast, in a raid boss fight, you expect to wipe a lot. That the fight is intricate enough that learning and mastering it will take multiple hours. It took us two or three evenings to refine our strategy and master The Lurker Below, and he's generally considered an easy boss in SSC."
He makes a few more good points in the article, including the fact that for casual guilds, losing time to trash mob respawns could be better spent learning a new boss. Obviously this affects more casual raiders than hardcore ones, but I think Coriel summarizes his points well and is worth a read.