There are a lot of different opinions about breaking in a new engine. When you buy a new vehicle from the lot they sometimes tell you about engine break in procedure. There is a section on it in your owners manual. Some say don't hold it at 65 mph on the freeway for, an extended amount of time, and others say that is just a wives tale.
I agree with the time and money being spent on a rebuild there are some nerves involved. Overall its an engine, and it is made to be used. As long as you are not abusing it during the first few thousand miles and after that, I'm sure 9 out of ten times everything will be fine with it. There can be defective parts, or just the right conditions that can cause an engine to fail, or parts of it to fail. But as long as everything is set right, and you are consciously taking care of it things should go well.