The cylinders are plated with a composite material and you can hone them if you want to, but the composite material (silicon/boron/carbide and other metals) is so hard that a typical glaze breaker or rigid hone hone will not impact the coating. From the pictures it appears the composite coating is worn through at the top of the cylinders. I suggest if rebuilding, to sent the cylinders along with the new pistons to a cylinder plating service to have the cylinders renewed and sized correctly to the new pistons.
It is recommended when servicing a plated cylinder engine that the cylinders not be honed when installing new pistons and rings as it is simply a waste of time, however, just to clean the cylinder prior to installation of new pistons and rings, using a green scratchy pad (Scotch Brite) to remove dirt and carbon.
