The nice thing about this idea is that none of the actual plans for the MonsterVerse franchise that currently exist negate it. Being a prequel means that the material is shielded from anything that happens within the continuity post-1973, so it should be safe from Godzilla vs. Kong (though it is worth noting we don't know the setting of that particular project just yet). If Legendary Pictures is looking for potential Kong stories to explore after the 2020 crossover movie, perhaps they could go back to Jordan Vogt-Roberts and let him execute his own designed narrative.