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Just been out to the shed and pulled out my set of 1009's and no holes in those locations, so I grab the 55thou cometics and same deal, no holes for the 2 outside water ports.
As the OP was trying to get across., is this a problem blocking these holes that are in the heads and block ??

You are exactly right, MLS gaskets are made out of stainless steel, very tuff, but they do not conform at all, head and block have to be straight and smooth. With a surface finish a lot smoother than what most old muscle car engines were from the factory. I have had this talk with several of my customers, price of gaskets, block and head machine work, most decide to stick with felpros.

Head gaskets are designed, in part, to control the flow pattern and volume of coolant between the block and heads. ALL the casting holes are intended to remove sand during the casting processes. DO NOT alter the head gasket's holes or else you WILL have cooling problems.

I was a former gasket engineer for a major mfgr... that was always (and remains) the #1 Tech Line question we received... regardless of the make/brand of the engine. The car manufacturers determine the casting holes and the gasket coolant holes during endless testing before mass-production.

The hole that is circled is supposed to be blocked off by the gasket.

It is not part of the normal coolant flow path.