I just came across this thread which is a few years old now but I thought I'd add my input anyway. I'm rebuilding a Mini Cooper S MK2 which I've owned for many decades and have had other elderly twin handbrake cable minis in the past as well.
The simple answer is that the two cables rubbing on the ridge of the tunnel underneath, just to the rear of where the cables go through the floor is quite normal. My Cooper S is no exception. You need to grease the area where it rubs and that's it. The cables do eat through the paint and wear into the steel where they make contact. Provided it's well greased, it will take a very long time before it really eats through the ridge.
After totally dismantling my car, restoring it (it retaind its original floor) I could see that the wear on the ridge in both cases was only a fraction of the thickness of the metal after 100,000 or more miles. You would have to clock up another few hundred thousand miles before it would wear right through. The ridges on the tunnel are there to add rigidity. That one also acts as a cable giude.
It's crude, but minis were built down to a price. Whether it was designed to be like this I don't know but my 1965 Hornet was the same. I hope this helps if anyone returns to this post.
Steve