I've always played it (both for Eldar and Necron) that they can choose. After all, the act of moving through a portal onto the board counts as movement (which is why all movement is measured from the portal/gate). The formation cannot fire obviously, but it is still left with the option of regrouping (removing BMs). This can happen often with the Necrons as there will frequently be unbroken formations off board with an array of BMs on them.
This may seem unfair that formations can rally off board but it doesn't happen often in other armies. For the Necrons, formations that are off-board count as destroyed for victory point calculations, so it is rarely an advantage for them to leave anything off board, especially as you get later in the game. One lucky hit on a carefully positioned Monolith and you can have all your plans go into the toilet.
