I'd like to third this.
I noticed when I was testing Thunders (from a Phaeton with Converted Hangar) in the simulator, that on Regroup and close to my target Atlas the Thunders would individually launch, spit out their Harpoon, and then land to rearm. Which made them completely ineffective against the Atlas. Switching to Engage allowed the active Thunder to start using its other weapons, but with the Phaeton's replacement rate down in the dumps, the second Thunder was unable to relaunch before the first (and my Phaeton's machine guns) finished taking the Atlas apart. Being able to command "stay docked" would allow me to launch the Thunders when they were both rearmed.
Also, the fighter AI seems to have no conception of "land for repairs". It can only land to rearm. Now, choosing to repair in the middle of a furball might not be the best of tactics, but a carrier that's unengaged might want to recover its damaged craft right then instead of waiting for the next engagement and seeing them finished off.