Several decades ago PADI adopted the mastery learning philosophy pioneered by Dr. Benjamin Bloom.My purely anecdotally-based speculation is that the two programs have a slight philosophical difference. PADI is all about "we can help the new diver overcome their inabilities/fears/incompetence and learn to dive." It's very similar to a K-12 education model. Fail on your first attempt, we'll give you more tries and remedial education until you're educated. NAUI gave me more of a "hey, that's ok, not everybody needs to be a diver" philosophy.
A quick summary of how mastery learning differs from traditional learning can be summed up this way. In traditional learning, time is the standard and learning is the variable; in mastery learning, learning is the standard and time is the variable. In standard learning, you teach for a specified period of time and then measure the result. If the student does not meet a standard, then the student fails. In mastery learning, you keep teaching and checking progress until the student meets the standard. It takes whatever time it takes.