You just lengthen the back of the car...
The 3" comment was sort of hyperbole. The 5 speed isn't longer but it's bigger up front. The additional bulk is taken up from the midmount forward and is concentrated up in the nosecone. Which is why you have to make room up by torsion tube.
The above example is an IRS box, but the swing axle is fundamentally identical from the side plates forward. The 5 speed is on the right with the silver parts being part of the Berg kit.
The shape of the 5 speed nosecone necessitates a new front mount, mid-mount, and bracket which you buy from Berg. You also need a new shifter.