There is no such thing as safe rounds. With things like Linked and Breach, I'd take on a battalion of stormtroopers before I got into the cockpit of a fighter. I'll take that flight of minion Ties over a basic freighter everyday.
Breach isn't that common among weapons able to target fighters, just warheads really. And Linked isn't an involuntary thing. If your GM is shooting missiles and activating linked on you often.. you may want to ask him what you've done to offend him.
Hahah I am the GM, and while I'm not out to kill the players, I am here to make things at least difficult for them. One of the good quotes I've heard is "The GM isn't trying to kill you, he's trying to make you a hero" (paraphrased from Critical Role). If you're flying against Z-95's expect concussion missiles, if you're fighting a Star Destroyer, expect turbolasers.
As long as you factor in the use of those weapons into the encounter design you're fine.