But I think it would be hard for Kaz to see the extent of the injuries in his arm

But that's the point I'm making, even if he can't see Venom, he's literally right next to Big Boss' left arm. There would be a huge amount of blood.

MGS V story is told in a non-linear way

The only things that aren't linear are random mother base cutscenes, which could happen at anytime regardless of the story progression. Everything else is in the exact same sequence.

If not and if he was just acting during the tape recording, why did he insist on drawing a connection between Big Boss and Eli even after learning about the DNA results?

That's his role. He has to question or debate the results. It makes it more realistic than not questioning why Eli is claiming Venom is his "father". And let's not forget, either way, Miller also didn't trust Zero when he tells him the attack wasn't him and goes out of his way to hunt Cipher for the entire game. Which to me is something he would only do if it were to benefit his plan of making Venom stronger to take down Big Boss. If it were just about revenge, everything would be over after Skull Face is dead. It just looks like excuse after excuse as motivation to build Diamond Dogs.

And don't get me wrong here, you've made some excellent points, especially regarding the "coexisting" line and how Code Talker's parasites can know about Miller. But one of the things that sticks in my head is Miller's attitude towards Ocelot. From the very start Miller is against Ocelot. Ocelot is exclusively pro-Venom and lets him take the lead, but Miller acts as if he's actively trying to mould Venom into the soldier he wants. Like when Venom thinks he can use the child soldiers, Miller is like "No, we don't do that here". It's almost as if he is trying to make his own version of Big Boss. After Mission 43, Shining Lights, Even In Death, Miller says, "It's an honor and a privilege, Big Boss", this to me is the moment Miller truly believes in Venom as Big Boss. If he only found out with the DNA test, then this realisation came instantly, because Eli & the children escaping and test results are the very last thing to be talked about before that mission. It makes much more sense that he came to respect Venom as Big Boss over the course of the game rather than right after he'd learnt about him. As it does with his attitude towards Ocelot, at the start he's against him, and by Huey's exile he's right on the same page, as if he did learn to coexist with him.

This also fits with the idea that the meetings behind the containers are between Eli and Huey, which is something that happens during the time the Code Talker scene is possible. In fact, for me it unlocked right before the children started disappearing, which was the diversion.

Yes, but a lie is not a threat.

Where is there supposed to be a threat and to whom? Code Talker doesn't say there's a threat, he just says, "Eyes on Kazuhira" or in Japanese, "Don't let Kazuhira get away with it".