At least the way I think about it, these analogies are neither accurate to the theory nor necessary to explain it to the layman. Let's look at it academically. If our technology had the capacity to completely simulate any sort of universe, you can bet a least one research team would do just that. Well, if you, like me and many others, think of the intelligent mind simply as a very powerful and self-aware computer capable of learning and abstract thought, and if the so-called universe simulated by researchers has a model of matter capable of creating the logical gates needed to replicate such a computer, and the simulated universe contains natural processes by which these logical gates might evolve, then you must agree that it is possible intelligent life may emerge in such a simulated universe -- no matter how different, similar, big, or small it is in comparison to our own. Then, following the same reasoning, you must also agree that there is the slightest possibility that the nested universe may produce one or multiple collections of intelligence capable of the same thing.
In this thought experiment, the simulation isn't imprisonment, doesn't violate a sense of self-awareness or free will, and doesn't even rule out the concept of a god or ultimate creator. It simply abstracts the container in which our universe lives from something mysterious to something relatively relatable to our current technology.
Another interesting thought is if we ever become capable of simulating such a universe, it seems much more likely than not we're also a simulation, since there's a possibility for each simulation to produce it's own simulation or collection of simulations.