Specific always trumps general. Yes, the rules state that a natural 20 is an auto-hit. That's a general, sweeping statement. For example, I could roll a natural 20 throwing a feather at a dragon from 5 feet away, but that doesn't mean it's going to be a damaging hit and critical.
Logic and common sense need to be utilized.
To that end, a Luckbender modifies the roll, not the result. Yes it achieves the same thing, but the skill specifically says that it modifies the triggering role, which is pretty straightforward. If the target rolls a natural 20, the Luckbender can use his ability to change the roll to whatever he gets on his 1D6. This removes the condition of always hit because the die roll is no longer a natural 20. This is also different from condition effects like blind. Rather than a condition in which the 20 signifies a lucky break, the Luckbender manipulates the universe to alter how things could have been. Think of him like a really, really limited Jedi. He can see the crit coming, so he used his ability to avoid the critical strike. He might even have been lucky enough to avoid the entire hit.
Anyways, as per the rules, specific trumps general.
Text from the ability:
Trigger: You, an ally, or an enemy in the burst makes an attack roll, skill check, or saving throw.
Effect: Roll 1d6, and either add or subtract the result from the triggering roll.