I used to be fascinates by this option in the command menu. I spent ages trying to put this to use, mainly to capture Shivan vessels because they'd always stressed the importance of it in FreeSpace 1. I always massively struggled to get it to work. Most of the time the ship in question would be destroyed, maybe it would have 3 engines instead of 1, maybe the docking ship jumps out etc.
There was one time, I think it would have been the Sixth Wonder where there's an NTF cruiser. I managed to disarm it, get one of the freighters or transports to go and pick it up, it went to it's warp point and jumped out with it. I was expecting a commendation from Command for retrieving a cruiser and bringing the crew to justice.
You can imagine my disappointment when neither command nor the debriefing even mentioned it.
I tried it with the Sathanas a few times, but it doesn't have an approachable dock point so it just crashes the game. I can't remember if that was something in a retail mission or something I set up myself.
It got me wondering what the point of that option was in the command menu was. Any captures of a ship would have to be scripted events, and the game doesn't really handle it that well anyway (if you're not sure what I mean, dock an Elysium to a Colossus and ram into the Elysium). I can't remember ever using it, all the capture missions in both games happened without your input.
Was it just a remnant from some older plans to have the player press the button?