Please check use cases below and just confirm if they are possible or not to be replicated. I think UC2 will be a problem for 3DX...
and UC4 is already known 3DX limitation. So you can ignore it. 

Prerequisites:
Model1 with MV1 Frozen and MV2 In Work
Model 2 with MV1 Frozen and MV2 In Work
Activity done in Native Client
Use cases should be working for both 1st Change Action and 2nd Authoring Context possibility

UC1: As a designer I shall be able to create physical product (EM-child from MAC) under an existing physical product (MAC - father from EM) and link Model 1(MV1 Frozen MV2 In Work) to its configuration context so that I can instantiate instances (Physical Product/ 3dPart) under this newly created EM later on, using Authoring Context Model1-MV2 or Change Action with Model1-MV2 applicability.

UC2: As a designer I shall be able to add second Model 2 (MV1 Frozen MV2 In Work)  to an existing physical product (EM-child from MAC) which already has Model 1 (MV1 Frozen MV2 In Work 2 from UC1) so that I can instantiate instances (Physical Product/ 3dPart) later on under it, using  Authoring Context Model2-MV2 or Change Action with Model2-MV2 applicability.

UC3: As a designer I shall be able to remove all instances from UC1 and UC2 so that I can revert the modification in case of mistake.

UC4: As a designer I shall be able to include back those deleted instances from UC3 so that in case it was not a mistake they can be back included. (I think here we have a ER with DS as they are not able to un-ignore ignored realized change under CHA, so you can skip this UC).

@BD and @VW