What you say is true, about the time window for the damage, however if the megaship tags a scout and then I kill it by removing 90% of its health, I think I am entitled to the combat bond, and that's what's been happening. I kill, no bond.
We were a group a ships attacking the Hydra (plus another Hydra, and a Medusa and a Cyclops before them in that specific instance) and we got the bonds for each and every one of them, except for the one that was hit by the cap ship.
It could be related, or maybe not, but it's the one thing that makes sense, based on all previous occurrences.
Edit: correlation is not causation, but since we do not have more data, it's not necessarily wrong to make this assumption, considering that it has been experienced consistently.