The original form of the Bostrom thesis is that, because we know that our descendants will probably be interested in running ancestor simulations, we can predict that, eventually, a very large number of these simulations exist. Thus, we are more likely to be living in an ancestor simulation than the actual, authentic history that they're based on.
If we take our simulators to be incomprehensible, computationally-rich aliens, then that argument is gone completely. We have no reason to believe they'd run many simulations that look like our universe, nor do we have a reason to believe that they exist at all. In short, the crux of the Bostrom argument is gone.
Thanks for the reminder.
I can see a case that we're more likely to be living in an ancestor simulation (probably not very accurate) than to be actual ancestors, but I believe strongly that the vast majority of simulations will not be ancestor simulations, and therefore we are most likely to be in a simulation that doesn't have a close resemblance to anyone's past.
Jonathan Birch recently published an interesting critique of Bostrom's simulation argument. Here's the abstract:
The paper is behind a paywall, but I have uploaded it to my shared Dropbox folder, here.
EDIT: I emailed the author and am glad to see that he's decided to participate in the discussion below.