All of the Hobie hardware is stainless. You may find discoloration on stainless parts because dust carrys metalic particals and will rust on the surface. We don't make rod holders, so those may have been something supplied by a dealer?
Remember that stainless is just that... stains - less. Not stain free unless it is carbon free, which is required for stiffness, pure stainless is soft.
As noted... likely carbon bits stuck in the stainless is all. Will most likely be discoloration and bleed rust a bit, but the screw will not rust away.
The screw is an Allan head stud threaded into brass.
88991215 SET SCREW, TI MAST V BRACE 1/4-20 THRD RLD, 17-4 SS
8050111 NUT 1/4-20 HX NYLOCK
You can coat with a number of different products to clean and prevent rust stains. We have a product called Magica that is... magic. Dissolves the rust stain and... gone!