The Matrix misses the point in a very important way.
In The Matrix the characters could easily tell apart the real world from the simulation, but the point of Simulacra is that you can't tell it apart from reality, not because there is a conspiracy that conceals it from the masses, but because simulacra replaces reality, conceals that there wasn't really anything "beneath" the simulation in the first place.
Indeed, that’s my feeling too: knowing Simulacra and Simulation I had expected that at some later twist it would have become apparent that ”the real world”/Zion/whatever would be somehow revealed to be itself unreal (in some ’indistinguishable and irresolvable manner) — and some have argued that Neo’s supernatural powers extending into the real world actually are ’proof’ of this — but that’s dissatisfying from a narrative standpoint. It’s almost as if the Wachowski brothers (later sisters) used the allusion of Simulacra and Simulation as a hint of stand-in for a ”brain in vats” philosophical work (which it most certainly is not) on the basis of the ”simulation” part of its title and relied upon their viewership to have no clue what a ”simulacrum” is to keep the in-joke viable.
To be fair, it did turn out that Zion was in a way artificial. A rebellion carefully cultivated by the Architect and the Oracle to maintain a cycle of destruction and rebuilding of the Matrix.
In The Matrix the characters could easily tell apart the real world from the simulation, but the point of Simulacra is that you can't tell it apart from reality, not because there is a conspiracy that conceals it from the masses, but because simulacra replaces reality, conceals that there wasn't really anything "beneath" the simulation in the first place.