Are you talking about capturing a vanilla ship like Crimsom Fleet, or Watchtower ships? Vanilla ships tend to take off if you engage the landing party in a firefight as they leave the ship. That tends to trigger the landing bay to close behind you and the ship to take off into orbit. What I do for the vanilla ships is to try to approach the landed ship from the side or back where the landing party doesn't see me right away. Then I'll rush the landing bay and enter the ship without getting into a firefight with the landing party. You'll still hear the claxon inside the ship, but usually it doesn't trigger the ship leaving for orbit. You then have all the time in the world to hunt down and either kill or capture the enemy crew. You can then capture the ship and set it for salvage. I'll then leave the ship and track down the landing party. For the Watchtower ships which always land a good distance away and then leave as soon as the landing party exits, I use this mod to control time: Slow Time SFSE
https://www.nexusmods.com/starfield/mods/2952 . If you're worried about mods messing with achievements, there are several mods on Nexus that fix that problem. So far, I've never had a Watchtower ship go back into orbit with me on board. As far as salvaging any ship that has gone into orbit, I think you're screwed on that one. It seems hard coded into the games engine that once you have to pilot a ship in space, it becomes your home ship. If you can pilot the ship, you simply land somewhere with a ships tech or a landing pad with a ship builder console. Then you switch back to your real home ship.