But quantum field theory is just a model — a model to explain some bizarre and counter-intuitive observations about the universe. It is pretty clear that QFT cannot be complete: How could the universe embed a random number generator? And the fact that it is irreconcilable with general relativity means that QFT is definitely not correct or not complete. And of course there is the fact that it gives a wildly wrong answer for the energy of the universe and what the cosmological constant should be.
The term “empty space” might actually make no sense. The interpretation that “particles pop in and out of existence” not only sounds non-sensical, but it is really just a metaphor — that’s not really what is happening. We don’t understand what is happening. So it makes no sense to make claims that “space is not empty”, etc. We don’t know what space really is.