So i was thinking of this quest this morning and something occurred to me. Venom's mindset and goals are a mirror match for Naked's with only slight surface differences at best, such as Venom not talking quite as much. Thanks to the way things were set up odds are good that if they were both put into the exact same situation as the other they would end up making the exact same decision, even if the reason they would make that decision is slightly different. Which means that in this alternative MGS universe we are in Naked would have been enclined to go the hero route the same way as Venom has, as such it would make sense for him to set up his long term plan in a way that complements Venom going full hero because that's what he would do.
That of course begs the question, what exactly is Naked's plan in this Au. After all in canon Venom went the mercenary route but in this AU he was different so he went the hero route, that being the case it would make sense that Naked is different as well. Therefore it would make sense for his method of bringing about Outer Heaven to also be different. After all having Venom build up Outer Heaven as it's secret leader would be much harder as a global hero then it would be as a world renown mercenary. And that's not even getting into the fact that Venom's first instinct as Big Boss was to destroy their own nuke and to start working towards ridding the world of nukes. Which means that would also be Naked's first instinct as well. That being the case it means that Naked would be extremely unlikely to develop a nuclear capable Metal Gear, which means he would never kidnap Dr. Pettrovich, which means Gray Fox would never be sent to infiltrate Outer Heaven, which means Solid Snake would never get assigned to finish Grey Foxes mission, and that would make the events of Metal Gear 1& 2, as well as Metal Gear Solid 1, 2, & 4 as a whole impossible.
Basically what I'm saying is I'm fairly certain we destroyed the Metal Gear Timeline moving forward as a whole on the first vote of the quest. Or maybe it's just really early and I shouldn't theorize about complicated plots before my first cup of coffee.