If they are totally seperate things, than what on earth does it mean to "count as a natural attack" for an effect. ALL effects that enhance a natural attack require that you have a prerequisite of having natural attack to enhance.
Under your logic, no effect could ever happen, because you don't have a natural attack to enhance.
A prerequisite for a feat is no different than any other prerequisite - you must have something before something else is allowed to happen.
Now if you could argue that what happens in the feat is not an "effect," then you'd have an argument with which I could agree. Unfortunately, "effect" is an extremely ill-defined term in D&D except in regards to "Spell Effect," which has nothing whatsoever to do with what we are discussing, so we must they were using plain english here and not a technical term.
Your argument is a "Catch 22".
1. You may only take this feat if you have a natural attack.
2. The monk's attack counts as a natural weapon for the effects of this feat.
3. The monk's attack does NOT count, though, because, until the feat is actually in place and active, he does not have a natural attack.
Huh?
More generally:
1. An effect grants a bonus to a natural weapon.
2. The monk's attack would count as a natural weapon for this effect.
3. The monk's attack does NOT count, though, because, until the effect is actually in place and active, he does not have a natural attack, so that he does not qualify for the effect in the first place.
Again, huh?