yeah its a little strange because JW takes place pretty much right on top of the park from JP, just in the future. So having a JP land and a JW land could have a harry potter type problem where guests just have to not care what "time" they are placed in when they enter the land.
The different timelines doesn't really matter as everybody knows they're stepping into a fake world. Being in the same location in two different places is confusing. The HE is genius in so many ways but if somebody goes to ride Gringotts in IOA and they're confused, they can easily move to the other park without leaving that world. Let's say Universal build that SFX JP coaster based on Jurassic World in the new park and they're wanting to ride in IOA, it's not an easy jump to the new park.