Problem with that 'test' is the logic chain is faulty.

Silas Beane and some of his colleagues have come up with a test that exploits a feature of said simulations; their need to be discretized.
That statement isn't true. Digital systems work discretely but you get analogue computers. Sure they still use electricity so would have a maximum resolution of 1eV (electron volt) but it's conceivable that some advanced civilization would be able to create a technology which would operate on energy(strings, quarks, whatever) at a more fundamental level. Thus having the same 'resolution' as the universe.

So a simulation need not be discrete, therefore proving the universe isn't discrete doesn't prove we aren't in the matrix.