is simply nonsensical to speak of entities in "another" universe simulating "our" universe, as the word universe already means "everything that exists."
This seems a silly linguistic nitpick - e.g perhaps other people use "universe" to mean our particular set of three dimensions of space and one dimension of time, or perhaps other people use "universe" to mean everything which is causally connected forwards and backwards to our own existence, etc.
If the Simulation Argument used the word "local set of galaxies" instead of "universe", would you still call it incoherent? If changing a single word is enough to change an argument from coherent to incoherent, then frankly you didn't find a fundamental flaw, you found a linguistic nitpick.
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.