According to the film's producer, the home version of the film was confirmed to be R-rated and due to the fight scenes going on longer than allowed for a PG-13 rating.
The extended scenes themselves won't be any different than the theatrical version, just them lasting longer is what triggered the ratings change.
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Producer Charles Roven says these scenes will not be gratuitous. In fact, he explains that the "intensity" of the violence in the extended cut matches what you'll see in theaters. An R-rating was imposed, then, because the scenes go on longer, thus, in theory at least, dialing up the potency even further.
"There's not a lot of blood in our movies," he said. "The ratings board also judges their PG-13 and R ratings by what they consider to be a level of intensity and how much that intensity goes throughout the entire movie. There are some pretty intense scenes in Batman v Superman, and if they went on longer and had that same level of intensity, that might cause the ratings board to shift their rating."
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http://www.gamespot.com/articles/bat.../1100-6435365/