Connecting rod squirt holes?

IT's just casting flash and has not one thing to do with spacing or fitment, AND if you get anal about it and grind them off you will very likely be changing the rotating assy balance.
Not by much probably, but still. (say a couple of ounces if four or five rods have those.

My own opinion on marking the rods and caps in that location would not be a very good idea.
When you punch a mark in that surface it will distort the machined flat mating surface a little.
Maybe if the cap and rod were bolted up to torque when you punch it, it might be ok but do it very light.

Obviously just one persons opinion.