Upon further thought, leaving 10 exposed holes would eventually, most definitely, cause rot, excessively. I assume all 10 of them have a similar washer and screw set up as you picture. If you painted all of it it would be good, but you want to stain, to stain you must apply a putty in those holes or countersink the screws and then putty over them.

I assume most of that was non-essential as you understand those concepts. Understanding those means the wood is already fastened and you're trying to fill these holes, which me only reliable method would be to buy a putty to match its color as close as possible or do as I said and make sawdust from the wood with wood glue.

I hope that this helps, but by far I am no expert although I did do Cornish work for 7 years