Okay, if someone has talked about it I couldn't find it with my Search-fu, and I can't find a specific ruling in the book.

How does Unnatural Characteristic (x) deal with an additional bonus for the same characteristic later?

For example: Chaos Space Marine gets Unnatural Toughness (+4), then pushes enough through Nurgle to gain the Mark of Nurgle. Does this now become Unnatural Toughness (+5)?

Initially I thought yes, until I read the Mark of Khorne entry where is says "The character gains . . . and Unnatural Strength (+2) if he does not already have them. Which he did when he chose Chaos Space Marine as his archtype.

They stack, the phrasing in the Mark of Khorne entry is like that because you can only gain Unnatural Characteristic as a trait if you don't have it, upgrading it from 2 to 3 for example is, semantically, not the same as gaining Unnatural Strength (1)