Here is a copy of the e-mail I recieved from Endyne:

Beam polishing can reduce the possibility of stress risers developing from flaws in the rods beam surface. If you beam polish the rods, all the grinding marks MUST travel from the small end to the big end of the rod, rather than across the rod, or it'll break, guaranteed.
We also recommend shot peeing the rods after beam polishing, and resizing the big end after new rod bolts are installed. You still need to keep an eye on the big end's roundness after sustained high rpm operation, as the stock rods tend to oval rather easily, causing the bearings to spin.

You see, it is not pointless. The rods will be balanced so that is not any concern. In order to install CTR pistons on B16 rods, you must machine the small end to fit them. If taking metal off the ends of the rods is soo bad, then why do people install the CTR pistons on B16 rods??? It won't have any adverse affects if they are balanced. As far as the looks of them, I could care less.