If the question is whether we only perceive and understand what we do because of how our brains are built?
The answer is that if something beyond the capacity of our brain to understand existed in reality, then we would perceive its effects on things we do understand. We would be able to conclude: we don't understand that. Not in the sense of we haven't figured it out yet, but that we have proved conclusively that it is non-understandable. And in fact, I highly doubt that such a conclusions would be accurate. If something has an effect on things we understand, then some component of it - the part that affects us - is understandable, if not at least random in the pure sense.
Next: if there is no effect we can perceive, then it is as if that thing does not exist. The brain, our universe, etc. are all that is.
Instead, I think there is just a certain 'way' to existence that has to do with what identity and definition mean. And those laws are fundamental. There is an alternative, I guess, but it's big dark blackness that is as infinitely consuming as it is infinitely minute. In other words, who cares about that anyway?