The damage bonus section simply says "...then each losing character takes one additional wound for each damage +1." So the way I figure it is, if a minion with damage +2 wins the skirmish, the companion will have to take three wounds. Sapling responds to the first; the companion did not take a wound. Second wound is taken. Third wound is then ignored.
Same for something like
Frenzied Attack. It says to wound a character twice. If the first wound is prevented, I think the second wound will be taken.
But, I'm just thinking about Lorien Protector. Does the fact that it has a very different wording to Armor mean that it would work differently? (Obviously preventing the wound on Lorien Protector means he takes no wounds).
Let's say a companion is killed in a skirmish and threats trigger. You can assign only one threat wound to a companion bearing
Armor, assuming no wounds were taken by the companion during that skirmish. The rest will have to be assigned to companions who can take wounds. In the case of
Lorien Protector, after he takes the first, he turns into a walking
Gimli's Helm--you can assign the rest of the threat wounds to him, and they'll all be ignored.