The SVN log says:
"Xordan fixed bug #2116: Natural Armour is now applied as a bonus to normal armour instead of being a set of armour worn in its own right and replaced when equipping other armour."
However, if we then look at bug 2116, we find this:
"By Xordan: Now it should pick the highest value of armour quality, either equipped armour or natural armour."
Perhaps Xordan can comment on how it was changed? In the case of the Kran, counting their natural armour is a bonus seems to make more sense than completely ignoring it when high quality armour is equipped.