When two plastic bases would overlap you just move the ship until both bases touch.
Because you don't have the possibility to lay down a 2-dimensional shipcard like in Wings of War this is a good rule. Normally we look at the playing surface as 3-dimensional space, so flying across another ship doesn't affect your movement. 'Standing on the same spot' should be possible but that would be too difficult to do in this game.
What bothers me a bit is the rule that you have to skip the Perform Action-step. Why did the game inventors like to give such a huge penalty to the moving ship? (And IMHO denying a ship an Action is huge).
You may say because the pilot is too busy avoiding a collision. But then again the game is 3D, why should the two ships are so close? Maybe they are miles apart on the z-axis.
Or you can say if a player flies that irresponsible he should be penalized. Okay, on the other hand sometimes you can't anticipate the maneuvers of all 4 surrounding TIE-Fighters.
I wonder why they made that rule and would like to hear your opinions. Actually I don't like the rule and consider to let the moving ship still do its action and only limit its movement and choice of targets.