Build pipeline and wrong values in OnValidate / ISerializationCallbackReceiver

I'm trying to understand how the build pipeline works in Unity after we call 'BuildPipeline.BuildPlayer(...)'.

There has been some weird behavior on our build machine where objects that implemented the ISerializationCallbackReceiver got calls to the OnBeforeSerialize and was causing null references. I've since removed any ISerializationCallbackReceiver to avoid these.

Now I've noticed that OnValidate has the same issue, where it gets called during the build process. In the OnValidate function the code calls a GetComponent() and the values inside the component that has been obtained are empty. (In this particular case a string variable).

 #if UNITY_EDITOR
 protected override void OnValidate()
 {
     Something something = GetComponent<Something>();
     if (something != null)
     {
         Debug.Log("OnValidate: " + something.id + ", gameObject: " + gameObject.name + ", scene: " + gameObject.scene.name);
     }
 }
 #endif

This results in the log-file showing lines of objects with empty 'id' values, while the gameobject name and scene name are printed as expected, after the BuildPipeline.BuildPlayer(...) call.

This is also having me believe that there is something going wrong where we are losing references to component references being stored (RuntimeAnimatorController) in classes that are only build through our build machine.

Extra information: I'm on Unity 5.6.3p2, build process is running through TeamCity. Build machine runs on Windows, as a normal process, not a service.