The idea behind using a size smaller prop during bench break in is to let the engine rev to its normal rpm in spite of a super rich fuel/air mixture. Not everyone breaks in engines this way and indeed the sky does not seem to fall when broken in otherwise.

If using the "wrong" prop size or break in procedure did cause sure fire falling of skys, then it wouldn't be so controversial.

The recommended prop sizes for various engine sizes are usually the ones that get the most performance out of the engines. Because modern engines often are tuned for lower rpm use than some of the older versions, the recommended prop sizes have crept up recently.