That's... interesting. Not sure why Universal would allow this, assuming they already had a deal inked with Legendary. And there are always conflicting reports regarding the rights to make a new Kong movie, whether they belong to Universal or are public domain. Apparently it's the latter.
Does it impact the ride? Not really, since it's blatantly based on Universal's Peter Jackson version anyway, even if they like to claim it's its own thing. It completely kills any notion of franchise synergy though, and there's a possibility they may even want to change the ride's name.
Also, this is a bit off topic, but King Kong vs Godzilla is seriously one of the stupidest ideas ever. It's already been done by the Japanese, and it was dumb even by old school Godzilla standards. Creating any scenario where a 30-foot-tall gorilla (that can be killed with bullets) can feasibly fight a 500-foot-tall lizard that literally breathes nuclear explosions is completely out of wack with the dark, mostly serious tones of both King Kong (as he's traditionally portrayed) and the current American version of Godzilla. What are they thinking?