By the book, there's natural armor and natural armor enchantment. The latter stacks with the former, just like enchantment on plate mail stacks with AC bonus of said plate. Natural armor doesn't stack with natural armor (just like if you had armor and mage armor). Natural armor enchantment doesn't stack with other natural armor enchantments (just like magic vestment doesn't stack with a permanent +1 on an armor). Most buffs (like barkskin and amulet of natural armor) should be natural armor enchantment.
Thus buffs should stack with armor skin (giving natural armor bonus). Not sure about something like Elephant Hide.
Now, how nwn2 actually deals with the natural armor ... Would be nice to know

According to nwn2wiki it seems natural armor bonus (as from armorskin) would properly stack with natural armor enchantment bonus:
http://nwn2.wikia.com/wiki/Natural_armor