The brief run in at the factory is not to just catch catastrophic failures! They are checked for oil consumption and fail if the rings don't seat, fuel consumption is checked, power within a certain percentage of advertised power is checked and limited by federal specs, oil,fuel and water temp is checked. Then an oil sample from each engine is sent to the met lab to be checked for ,iron,chrome, alum., copper,water, fuel etc to make sure there are no problems. There is one engine per day selected at random for an 8 hr test at full load and then torn down and checked 100 percent by a mechanic,an inspector and engineer and a product quality man and then reassembled and tested again before shipping. There is also one engine per week selected for a 100 hr test and then checked 100 percent. These are known as bargain list engines and would be the ideal one to have as they are cheaper because they cannot be sold as new and have been checked 100 percent and retested again.
Diesel engines are made to run. If you are being told that you need a long break in period you probably have some gasoline engine quality parts in your engine (in my opinion). GM has done this in the past and it didn't work out too well. Run it like you are going to 50000 miles from now and you will be happy. One problem with babying a diesel engine is slobber which is usually corrected by running the engine with a large load. You are probably not hurting it with a long break in but you are not getting your money's worth out of your fuel or your investment.
Just an opinion from someone that has spent 35 years in the machining,assembly,test,quality control dept. and research as well as process development as a manager and hands on in the engine division of a major engine supplier to the trucking industry and the industrial world.
Do what makes you happy, you have still made a wise decision in investing in a diesel.