When making the summoner's eidolon, the armor bonus it gets says, "This bonus may be split between an armor bonus and a natural armor bonus, as decided by the summoner."
Is there a difference?
Yes, but I don't think there will be a reason why you would choose to make it an AC bonus instead of NA bonus.
If you make it an AC Bonus, spells like Mage Armor would not affect it unless the AC was 3 or less, except in instances of combat involving ethereal creatures.
Most spells NA bonuses will stack with pre-existing NA bonuses.
that is just off the top of my head... Not much is left up there though, so someone may have better insight.
Brilliant Energy Weapons (granted no player I know wouldn't cash such a thing in to buy something else, but I have occasionally seen DMs give them to NPC's anyway) ignore Armor Bonus but not Natural Armor Bonus.
Armor Bonus 0
Natural Armor 2
The main reason you would want to draw a distinction is to determine what other sources of AC stack with your bonuses. For example, wearing full plate stacks with a natural armor bonus but overlaps with an armor bonus.
There are a few other fringe applications, such as the brilliant energy weapons listed above.