I disagree with "not at all", to the extent that the Matrix has probably much less computing power than the universe it runs on. Plus, it could have exploitable bugs.
This is not a question worth asking for us mere mortals, but a wannabe super-intelligence should probably think about it for at least a nanosecond.
Hell, it's definitely worth us thinking about it for at least half a second. Probably a lot more than that. It could have huge implications if we discovered that there was evidence of any kind of powerful agent affecting the world, Matrix-esque or not. Maybe we could get into heaven by praying to it, or maybe it would reward us based on the number of paperclips we created per day. Maybe it wouldn't care about us, maybe it would actively want to cause us pain. Maybe we could use it, maybe it poses an existential risk. All sorts of possible scenarios there, ...
Although it regularly discusses the possibility of superintelligences with the power to transform the universe in the service of some value system - whether that value system is paperclip maximization or some elusive extrapolation of human values - it seems that Less Wrong has never systematically discussed the possibility that we are already within the domain of some superintelligence, and what that would imply. So how about it? What are the possibilities, what are the probabilities, and how should they affect our choices?