Not exactly sure what they mean there, because on this page: https://developer.mulesoft.com/docs/display/current/API+Gateway they also mention this:
Note that the API Gateway, because it acts as an orchestration layer
for services and APIs implemented elsewhere, is technology-agnostic.
You can proxy non-Mule services or APIs of any kind, as long as they
expose HTTP/HTTPS, VM, Jetty, or APIkit Router endpoints. You can also
proxy APIs that you design and build with API Designer and APIkit to
the API Gateway to separate the orchestration from the implementation
of those APIs.
So both methods technically allow you to separate API from orchestration, as your API gateway application could simply proxy another Mule application elsewhere that performs the orchestration. But my understanding of the two options are:
The API gateway is a limited offering that allows you to use a subset of Mule's connectors, transports and modules such as ApiKit and HTTP, it allows you to expose and API then use http to connect to whatever backend systems you want as a proxy and perform the orchestration in the API layer.
By using the Mule runtime operation, it gives you much more flexibility and allows you to compose as many applications as you want using the full range of connectors etc. and separate out the different aspects of your applications into as many layers as you want as separately deployable entities that you can deploy to on-premise standalone instances or Cloudhub etc.