I mean, I get some issues between producer Kojima and him not writing or directing it. But he DID insist that 4 was not to be fully worked on until the story for this game was finalized. In addition, he himself says the "Core Story" IS canon. It even makes a plausible point of Big Boss's time between the Peace Walker and Snake Eater incidents. Both games see Snake in latin America building a small band of soldiers to create a force strong enough to take on the respective threats. Not to mention how in Peace Walker, Miller says something about "leaving behind" the San-Heiranimo events. Indicating that it did, indeed happen according to Peace Walker and the location was a part of the Metal Gear world is at least a vague footnote in Naked Snake's lifetime. Oh, and the biggest elephant in this crowded room. Snake's MSF forces are seen in the beginning of the game, meaning he had already formed the unit before the opening ensued. Why wouldn't these guys have been remnants of the unit Snake created in 1970?
In addition, why should the opinion of one man matter? Just because Hideo Kojima doesn't like the game (at least not as much as the ones he wrote/directed), that doesn't mean that he is the decider on what is canon and what is not. Same with Metal Gear Rising: Revengeance. On the other hand, Metal Gear Ac!d 1 & 2 do contradict the storylines of the other games. The former game starring Solid Snake in 2016 after he is supposed to have died. The latter shows us a clone known only as Snake.