I've yanked quite a few stumps with a BB. That being said, the possibility of damage does exist.
If you pull forward with the teeth down, you'll rip through the roots of most 3" diameter trees with no problem. Just go slow so that you don't mess something up. And never use the outside teeth - the two center ones are the only ones you should use, or you'll tweak something.
When working with stumps up to 6" diameter, I snag the root, then lift the BB. This action will not break many roots, but if you back up slowly while lifting, it will tear part of the side of the root. If you repeat several times, you'll eventually break the root.
Now, what's my BB look like today? Well, the first very large roots I tackled with the BB were way too big. It was a 24" diameter stump, but it was dead for many years, so I thought the roots would be soft. After "jerking" into the roots many times, the slots that hold the two center teeth became elongated. Those two teeth now angle back further than the outer ones. No big deal, but it taught me to be more careful.
Yesterday, while helping a friend (he was also on a 'bota), I was pushing dirt backwards with my BB, and started spinning. I thought that I was just pushing too much dirt, so I continued pushing slowly, while slowly raising the BB. Then I heard a strange sound, and saw the whole BB being bent down to a 45 degree angle! It turns out that I snagged a hidden stump with the rear blade. Paint fell off in several places where the frame got tweaked. To fix it, I hooked the stump with the front balde on the BB, and it easily bent back into shape.
You'll notice on the KK brand of BB that the upper and lower members are connected only with the 3 PT pins, and are not welded. This allows the two members to go "different directions", i.e. the pins act like a hinge. If they were welded, it may be a better design... OR, you could end up damaging the tractor. I don't think I'll be welding those spots.
I've used my tooth bar to break roots as well, but the short teeth don't allow you to get to the roots next to the stump with the center teeth. You'll be tempted to use the teeth on the edges of the bucket, but then you risk bending your FEL, or worse, rolling the tractor. Whatever you do, make sure that you use the much stronger "curling" action (with the bucket on the ground) rather than the "lifting" action.
Even the little 'botas have enough poop to damage themselves or the implements being used. Always try to work in slow motion to limit potential damage.
Good luck.