But that's the answer. What is required is simply a way of specifying that models that overlap should not be combined but, instead, they should be butted up to each other so that they can be easily separated. One way of doing that would be to add a per-model option (could be added to the object position/scaling dialog) that specifies that if this model overlaps others, then the other models should be subtracted from this one. Setting that option on a mouse ear model would stop it being integrated with the model it overlaps.
So the feature request changes to add the ability to specify that a model will not be merged into other models it touches but it will have the portion of its volume that overlaps with those other models removed. That would be a lot simpler to implement than a whole mechanism for defining mouse ears and positioning them.