I love kojima, but i think many fans try to put every decision of his as some grand scheme , especially in a game like MGS V, where the development of the game made it impossible to be finished and many plot threads and ideas were left unfinished. The story implies some sort of war happening in that area of the game, yet we never see anything other than patrolling units. The world of red dead redemption is hostile, you see people getting attacked by animals, the story of the characters show how harsh the wild west life could be, in mexico there are often civilians being executed by the army, the rebels trying to fight the army, and others.
I think that if kojima wanted to convey this feeling you described, we would notice it much more easily.
That's not a grand scheme. He may or may not have planned all of this, it doesn't really matter to me or to any analysis. But yes how the development was conducted is important, it would require to do in detail on how in may have influenced some aspects.
About the war, I believe he didn't went the RDR way because that's wouldn't be the proper way. A war is not like a wildlife. Some games do it that way, with combat everywhere (Far Cry is the master of this). That doesn't really work, it's artificial. Kojima is more subtle than that (war sorties by audiologs, soldiers, documents for instance, and all the main missions that take place in the open world). Maybe it was too radical or unfinished but it was, I believe, the right way to do it and the right way for him to do it(knowing all he did as a game designer and game director).
Although that's a very complex game and I only focused on the open world aspect. The other main aspect would be how you become Big Boss thanks to the gameplay and that fits well with the story too. Or how he used the online aspect into an endless war.
This is hard to evacuate as much as possible the judgement we do (is it good? is it fun? etc) in order to focus on a more suble and nuanced focus on how things work, why do they work like these, what were the intented effects, what methods were used, how does it fit with the story and what the game tells us... It isn't easy and I've just scratched the surface of the topic (thanks to the critique I read)
/end of the off-topic for me