The most subtle aspect of the question is the "coordination" step (
http://ncatlab.org/nlab/show/coordination) that takes one from a mathematical formalization of some physics to the corresponding perception of conscious observers living in that physical world. It is not a priori clear that if a mathematical theory models space(time) as a continuum, that this is also what observers in this world will perceive.
Take the example of phase space. Common lore has it that after quantization it turns from a continuous smooth manifold into a non-commutative space. This assertion is what much of the effort towards noncommutative models of spacetime takes its motivation from. But it is not unambiguously true!
Namely the folklore about phase space becoming a nononcommutative space draws from one of two available formalizations of quantization, which is algebraic deformation quantization (
http://ncatlab.org/nlab/show/deformation+quantization). There is another formalization, which may be argued to be more fundamental, as it is less tied to the perturbative regime: this is geometric quantization (
http://ncatlab.org/nlab/show/geometric+quantization) (John B. knows all this, of course, I am including references only for this comment to be somewhat self-contained just for the sake of other readers).
Now in geometric quantization there is no real sense in which phase space becomes a non-commutative space. It remains perfecty a continuous smooth manifold (infinite-dimensional, in general). What appears as a non-commutative deformation of the continuum in deformation quantization is in geometric quantization instead simply the action of a nonabelian group of Hamiltonian symmetries (conserved Noether currents, in field theory) on the continuous smooth phase space. And yet, where their realm of definition overlaps, both these quantization procedures describe the same reality, the same standard quantum world.
That is incidentally what the infinity-topos perspective thankfully mentioned in the article above, makes use of: geometric quantization, as the name suggests, is intrinsically differential geometric, and as such lends itself to be formulated in the higher differential geometry embodied by cohesive infinity-toposes.