But the Jurassic Park island in IOA doesn't take place on Isla Nubar, it takes places on a new island called "Isla Aventura". However, I believe that fact is only still mentioned in a few easy to change places and a majority of regular park guests are probably completely unaware of the island's actual backstory - they just see it as an area of the theme park with Jurassic themed rides. Universal doesn't seem to acknowledge it at all on their website or promotional materials, so they could easily just pretend that whole backstory never happened.
But like you said, I honestly don't think a mismatch matters much either. We've seen the crossover in the movies so I don't think having both is really an immersion breaker. This is their opportunity to make a new backstory for the land and sort of reinvent it and I can't wait to see how they pull it off.