This is probably awful so I'm not really suggesting it, just speculating.
Spawn alien bases around globe as "airports", roll a cutscene "you depart from x to y" with a nice few of slides like...
-you drive to the airport-
-you check your luggage in, you take nothing suspicious-
-you fly off to your destination-
In addition spawn alt mission if the player is close enough to drive to, bonus maybe being they can bring what they like.
-insert desired mission-
missionXCompleted research awarded
baseSelfDestructCode destroys all airports (to remove mission).
Obviously an actual flight in a civilian aircraft is a little too much to simulate, as would be the passage of time, so probably the most accurate way to portray those steps is to just average out the the x-hour drive and y-hours of flight. as you do now.