That is the true meaning of inter-dependence of energy storage elements: in the model they are not distinct energy storage elements, despite appearances to the contrary. These two modelling approximations — rigid-body models and time-derivative operations — are intimately related.
This is a typical consequence of dependent energy storage elements and, as one might expect, in more complex systems the algebraic manipulations can become formidable, even prohibitively so. It would be useful to know about dependent energy-storage elements before attempting to derive equations. How may we do so?
Because the two energy storage elements in this model are not independent. Because of the one-junction, the velocity or momentum of one determines the velocity or momentum of the other; given the masses of both bodies, knowing the energy of one is sufficient to determine the energy of the other.
Every energy-storage element which can be described using an integration operator should be. It will require one initial condition to determine its constant of integration, and therefore will give rise to one state variable; energy storage elements which have integral causality are independent.
Conversely, any energy storage element which must be described using a derivative operation will not require an independent initial condition and therefore will not give rise to a state variable; energy storage elements which have derivative causality are dependent.
So I would say that the two inductors together contribute only one effective energy storing element. Also, how sure are you about the correctness of the mechanical to electrical conversion?