of course you could always cut out the back part of the armrest, finding some thing to use a trim to cover the place where you cut is the tricky part.
ive done this on a different car for a friend, and built a box that had a port that lined up perfectly for it.
but as a much better solution
Just remove the stock 6x9s in the rear deck and those will act as blow-throughs into the cabin.
1st, the square area of the sub cutouts is much larger than the section of the armrest. more area, more flow, more sound.
2nd, it will be much easier to make look good than the armrest.
3rd, if your building your own box, you can always make the ports directly under the sub cutouts.
my subs are facing up under the factory cutouts, since they are facing right at the way out, there is very little pressure in the rest of the trunk, making everything much less likely to rattle, and there is very little difference in sound levels with the seats up or down.