My 2 cents on the matter... I'd go for separate packages.
The OGCAPI modules are right now pure protocol implementation, while the
"engine" is really in the classic OWS services.
The pure protocol part is the one that is most subject to change, and if
they ever do a v2 it will be (by semantic
vers
I am looking into the best approach to handling versioning in the new OGC
API endpoints from a code maintainability perspective.
In WFS an "adapt" call is used to match a request to an embedded subclass
of the request type (see for example
https://github.com/geoserver/geoserver/blob/de184b2f9ed9a8