If an attraction is hitting close to the number of visitors that it is designed to put through in an hour, operations managers really don't care that much about the wait time - they're putting through everyone they can. If more people than that are showing up, well, there's nothing ops can do about that. (Except make a case for more building attractions, of course!)
The problem is when you're not doing hitting that number, and the number of visitors you're putting through every hour is far below your capacity. That was the problem we had on Tom Sawyer Island with the overloaded rafts - a really low percentage of "theoretical capacity."
So if we hit our highest possible capacity numbers, and that draws people from other attractions or off the street into our queue - fine. We'd rather have a 20-minute wait with us putting through 1,000 people per hour (for example) than a 15-minute wait when putting through only 500. Wait times are only held against operations managers if they're putting through a low percentage of their operating capacity.
Is there also a factor in which the length of a waiting line serves as a deterrent to other guests choosing a certain attraction? If so, then any attempt to reduce wait times by packing the raft might be offset somewhat by additional guests entering the queue because it is no longer unattractive.