Con rod polish

In my experience,  they all look like your first picture, 88ss included. Any that are polished have been done by POs.

In his book about Dommy tuning Paul Dunstall talked about polishing controls to remove stress-raisers, so obviously they must not have been from the factory.

Polished my Dommy rods 30 years ago ,  still hanging together. 

I consider it good practice to protect the shanks of conrods. These can easily get knocked as you say when lifting the barrels, also the pistons themselves will inevitably swing and their skirts then clip the rods- not good for either. I always wrap some rag around the rods, stuffed up inside the pistons to prevent that. Will need to support or suspend the barrels to do so, unless a spare pair of hands is available!

If the bottom end is to be left exposed for a while with the pistons removed, empty toilet roll tubes make handy protectors.

On the matter of polishing, it is many years since I last read Irving's "Tuning for Speed", but I think it says when filing off the flash along the shank, to do so in a single direction only, ie not simply across or with an up & down motion.

If you ordered a new Norton to Sports Special Specification from 1958 onwards, for lots of extra cash you would get an engine with all kinds internal 'go faster' goodies. This would include HC pistons,  polished cylinder head ports, polished crankshaft and polished rods.

This Factory extra was available up to the close of Bracebridge after which only the 88SS and 650SS  were kept on the 'road' models list with the Atlas being added a little later. However, the SS suffix, although standing for Sports Special did not include any significant tuning.