Hm. I'm seeing a lot of problems here, but they have less to do with your story idea and more to do with how you're going about the brainstorming process. Mainly I'm echoing Clayfinger that starting with a large project is a risky idea, and you learn a lot by starting with smaller ones.
First off if you're considering embarking on a long project I strongly recommend Mystic's
Guide to Writing Epic Storygames. Tons of fantastic advice in here.
Here's the main things that concerns me about your idea:
1) You have a big idea that requires a long game, but you don't seem enthusiastic about all the material you'd need to come up with to fill it. You like the idea of an epic scale 4th-wall breaking confrontation that involves both character and reader. But I'm not getting the sense that you're at all excited about the biblical sub-stories you'll have to write to support this, when those are A) the chief focus of your prompt, and B) the actual meat of the story. No matter how epic the building hidden background plot is, this game will not work if passion and craft isn't invested into making the foreground plot genuinely compelling in its own right.
2) There are inherent limits to a 4th wall breaking story. They can be very good, but you can only 'involve' the reader so much before they remember they're reading a fictional story and no eldritch monster from it can ever enter our reality. The best 4th wall breaking stories are the ones that work with that limitation (or at least reasonably cover it up) rather than asking the reader to conveniently forget about it.
3) It's concerning that you're asking for input from others about broad topics like branch structure, variable decisions, and the overall direction of the story. Either A) You're seeking very basic advice on how branch structure/variables/storytelling plots work, in which case you haven't put in the requisite work to build a complex game like this anyways, or B) You know your options, but don't actually care enough about your idea to have strong feelings about how you implement it or where you take your story.
If it's option A, the good news is we have articles on this stuff:
This article has a link to an article that explains the major types of branching narratives, and the
help & info section has a lot of articles that can give you an idea of what you can do with variables. You can explore these resources and figure out how you want to use mechanics to enhance your storytelling. But it's not likely that you'll be able to implement this at the scale you want to, on your first try, within the span of the contest.
If it's option B that's less fixable--it sounds like you just don't care much about your idea, and you'd be better off picking something you DO have strong opinions about than asking other people to fill in the gaps. Ultimately you are the one who will have to write your story, and it will only happen if you yourself are passionate about every writing decision you make.
EDIT: Just say your response to Clayfinger. It's true that playing it safe doesn't promote growth. But over-reaching doesn't either, it just leads to collapse and burnout. There's a sweet spot in the middle where you're pushing yourself just past your previous limitations where the most growth happens. In your case, if you've never written a storygame before, just getting one finished is the limit you're pushing. You'll learn and grow plenty by picking a small idea and putting in the work to do it justice.