The modifications that PaulLach made are from this post. I tested and confirmed that the changes worked on the command ships. I did no further testing after that, which failed to show the bug about other ships being able to capture ships. My "fix" seems to cause a bug, which means it's not as good a fix as I thought.
I just tested my "fix" again to get more information. I started with the survey ship, which doesn't have the ability to capture ships. I used it against space pirates. It didn't capture any. I then used the command ship The Claw, which has a 25% chance of capturing a ship. It didn't capture the first pirate ship, but it did capture the second. This all seems normal.
I then used the survey ship again. It did capture a pirate ship this time. I then made a fleet of the two captured pirate ships and attacked a small precursor sentinel ship. It was captured. I captured every ship after that despite using ships that don't have the capture ability.
This indicates to me that the 100% chance to capture was activated for all ships. Since this happened while using a mod with my "fixes", it sure looks like my "fixes" are bugged.
My "fixes" are based on the scavenger ability for the Snathi Revenge from GalCiv3. They have the scavenger ability for the faction. I added a section that included <TargetType>Faction</TargetType> and changed another part from <TargetType>Ship</TargetType> to <TargetType>Faction</TargetType>. One or both of these uses of Faction could be the problem with my "fix". I plan to do more experimenting, but that will be later.