Hello; It’s an interesting issue.
Unfortunately, that is too rooted in Blender’s UI. As you mentioned, Local Coordinates (Local Space Transforms) won’t be affected whenever the thing is Automated by something such as a Parenting Relation or a(n) Object/Bone Constraint. This often creates great confusion in Rigging, in several aspects.
The good news, is that, there exist a few types of manipulation which bypass that ‘Automatic Local Coordinates Inercia’, so that it IS actually possible to Manually Pose a Controller somewhere, that will Automate the Posing of its Dependent element, by actually making changes to its(their) Local Coordinates indirectly, literally, as if the user was Posing such Dependent elements directly.
One way to achieve that, is with Drivers to the Transform properties. But this will render the element itself Unposeable directly (Manually); however, additional ways of Controlling it indirectly are still stackable.
Another way (a bit far away than your Cubes’ case), that I know, but that is for Skeleton stuff mainly on Pose Mode, is a special Inverse Kinematics solution; the in-built Auto IK Option, affecting any FK Chain relying on Connected-Parenting, while employing adaptive Auto IK Length. All the Bones participating in the Posing of an IK Chain from Auto IK Option, Transformed just as if they were being directly, Manually Posed --making actual changes to their Local Coordinates. This special feature won’t occur in the case of Inverse Kinematics made with IK Bone Constraint.
There might be other solutions… but I do not know for now.
Here is what a Setup with Drivers can provide in the Cubes case:
Just manually match Copy as New Driver from medium Cube’s Transform (Locator-Rotator) to the other’s (small BlueCube) with Paste Driver.
In this particular Setup, only the medium Wire Cube (“Locator-Rotator”) is Parented Offset to the large Wire Cube (“Locator”). And the small Blue Cube (“BlueCube”) has got a Copy Location Constraint Targeting the medium Cube; that allows the large Cube to be a MTR Locator for both, without Stacking/Double Tranforms.
Wait… there is a mistake in the Setup. As I’ve mentioned, Parenting Relation and Constraint doesn’t affect Local Coordinates of Dependent elements. So, Posing the large Cube is not working (in order to update the BlueCube Local Coordinates Location Transforms values, although Manually Posing from the Driver medium Wire Cube does register. Might have to investigate further, maybe a full round of (Non-Stacking!!!) Drivers between different Cubes… Unsure now. I guess you’ll have to figure it out. Hope that helped. 
