fix(api-machinery): Fixes patching for unstructured objects

CRDs and other objects seen as unstructured cannot use strategic
merge patching. It has never been supported on CRDs. Previously,
cases like unstructured objects could have caused an unregistered
error. This is no longer the case.

This change explicitly looks for unstructured objects and handles
those using json merge patching.

Closes #3382

(cherry picked from commit e6137ff0)