The counting is done inside a chosen reference class of "human civilisation". Pick one definition that makes sense, and the argument applies there. So yes, by definition you are counting simulations of civilisations, not of simpler phenomena (say ants-only simulations).

In the space of all simulations, we are very likely to be pretty close to the simpler possible simulation inside the reference class, but there is no way of probing this. What we can do is make comparison with more complex versions of our current reality. If you think that we are not that simple, then you should believe that we are not in a simulation after all.

True, the universe may have been started 1 second ago, but among all the 1-second simulations some are simpler than other nevertheless. For instance a 1-second simulation in which we have colonised the entire milky way is far more complex than our current experience.