This trope shows up in so much sci-fi because it's a pretty quick way to undermine any philosophical questions. What's my purpose? To help run this simulation. Maybe I'll live long enough to find out when the outside computer shuts us down. It's never bothered me personally, because there's not a lot to be done about it. On some level, though, it's a though experiment that I didn't have a good answer to.
Of course, it's still unprovable: the outside simulation might have oodles more atoms than our universe, or different physics, or magic! But that's fundamentally less interesting than knowing there's a "higher" universe with roughly the same physics. That looks much less likely at this point.
It's really cool to read an argument that so strongly disproves something I thought was untestable!