It looks odd that $ramlData['resourceTypes'] is processed twice. This doesn't feel right.

Sorry about that, removed unnecessary code.

Readability can be improved by extracting the if body in a submethod, eg private function isRaml08(string|int $key): bool. Indentation levels can also be simplified by replacing the else consrtuction with continue as part of the if.

The final code will read something like:

foreach ($ramlData['resourceTypes'] as $key => $resourceType) {
  if ($this->isRaml08($key)) {
    ... // logic to process 0.8 resource types
    continue; 
  }
  ... // logic to process 1.0 resource types
}


...


/**
 * @param string|int $key
 * @return bool
 */
private function isRaml08($key)
{
  return \is_int($key);
}

Done. To reduce cognitive complexity we can move out this part of code in "getKeydedResourceTypes" method.
As we need exactly one or two cycles on resourceTypes, there are almost nothing to improve in code itself. Maybe recursive getKeyedResourceTypes call will look better but it leads to unnecessary array_merge for v0.8.

I don't think a recursive approach is the best one here as there is a known and very low number of iterations. A recursive approach can easily clear the way for otherwise broken, over-nested resources.