I think you bring up some good points, but overall I disagree with your above statement. In the History of Nebraska Offenses thread, I provided data showing the total defense ranking for Nebraska from 1989 to 1997. You will find that from 1994 through 1997 Nebraska had a top ten offense and top ten defense every year (provided some assumptions about 1995). Although Tom Osborne was not running Navy's current offense exactly, I think it would be fair to say that the Husker defense practiced against an offense that was also decidedly one-dimensional, and they did well by my standard.
I would also point to the head to head matchup between UCF and Navy, I realize the sample size is just one game, but the score was 31-21 UCF. While Memphis (which runs a similar offense to UCF, so according to your argument the defense should be better prepared) lost 40-13, and 62-55, and in 2016 won 73-56. This seems to point to the fact that the type of offense you run, doesn't necessarily dictate what your defense will be better prepared for.