There are ways to make it work. The Solid Snake mission can take place months or years after you stop controlling Big Boss, so the areas can be remixed and new elements can be introduced so that you don't actually know much going in that kills the sense of exploration or progression. It doesn't have to be 1:1 with how you built it up at all, but it could give you certain advantages to make an otherwise insurmountable task more manageable.
Having this enormous war machine at your disposal as Big Boss, rescuing and recruiting badass characters to fight by your side, given every advantage in the first half of the game as this leader of men, and then having it all stripped in Chapter 2 as Solid Snake, fighting Big Boss's charismatic comrades as boss encounters (who you as the player relate to and feel for because of the first half) and desperately scrounging for weapons and items that you can't have supply dropped to you on a whim...and then winning anyway, against all odds.
That completes the circle. It shows why Solid Snake is the namesake of the series. It's ambitious but plausible. Mother Base ideally wouldn't be a lame empty oil rig maze in that case of course, and the people you recruited also wouldn't all have randomly generated names and no personalities, and you'd have to scale back the Big Boss portion to probably not have the open world elements but be a series of story missions like Ground Zeroes. But it's plausible and I'd take it in a heartbeat.