Normally when you blow up a ship, it falls to pieces and the parts are all scattered to the winds of space.
But when you blow up the Flagship, pieces fall off while the rest of the ship jumps away. Now I'm pretty sure that's not possible to do for regular ships so I'm suggesting (and probably making at some point) something that might just imitate that escape.
The idea is this:
The ship I create has multiple gibs which stack underneath each other, with the main gib being a massive gate.
When the ship is destroyed, this gate gib appears and moves quickly through the ship. The other pieces "vanish" by being beneath the pieces before, but the effect should look like the ship is jumping away rather than blowing up.
I'm not good with gib direction or velocities hence why it's only a suggestion but I might just create it myself (as my one or two Youtube fans might have realised there's some sort of storyline going on with my videos and what better way to develop it further than to create an always-recurring ship out to kill the player?)