If the material that these fasteners pass through is not cored, there really is no need to fill the holes with epoxy. Unless you do not plan to reuse them, and instead plan to tap new holes.
I assume there is no coring there, otherwise the factory rep should have urged you to check the condition of the coring before resetting the rubrail fasteners.
If it's solid laminate, I would go with the factory rep's suggestion of 5200, MAYBE downgraded to 4200 if you think you'll need to remove the rubrail at some point.
Even if you fill those holes with epoxy, you will have to wait for it to set-up before you sink the fasteners into it again. And then you will still need to use some kind of waterprooof, durable bedding compound when you tap the screws back in.
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Pacific Seacraft Crealock 31 #62
NEVER CALLS CRUISINGDAD BACK....CAN"T TAKE THE ACCENT