It might work if you use the "save state(.sav)" mission file instead of a normal ".mis" file. What you have to do is create a mission that has you on short final to land on the Kuznetsov, land, taxi to where you want to start, and configure the jet how you want it. Then hit "ESC" to quit and when the exit dialog box comes up click on "Save". This willl create a new file with a ".sav" tag.
Next is to load the .sav file and you will start in the cockpit where you parked on the deck. The key for this is to delay the timing of all other mission events to start after you have landed and positioned on the deck. This works on the ground and I'm sure it will on the carrier.