We have to remember that the NFL, after everything is said and done, is a business. They want to make money any way they can. A great way to do that is by having its teams score lots of touchdowns. But not just any touchdowns: passing touchdowns. There's nothing as exciting to watch as a quarterback throwing a hail marry into the end zone and having the receiver diving for it. Those kinds of plays are more likely to happen if the ball is broken in to the quarterback's liking.
The ruling seems weird, but that's probably why the NFL allows its teams to supply their own game balls, instead of providing fresh ones for every game.