Ozbuzz, I'm really just starting out.
I read about it on Michael Bush's website and on the Natural Beekeeping forum.
When the bees make it their own way, they might make a lot of drone cells, and they might make the workers cells smaller, and the cells sizes might vary across the comb. I trust they know what they're doing better than we do.
As well as not having to buy wax, I can phase out the old combs. Might be good for disease control.
I've had some cases of bees building from the edge of the frame, or building upwards from the bottom in supers, but mostly no problems.
One time I put in some frames with foundation and the bees chewed out all the foundation and used it somewhere else, and then made the combs. :)