A consequence of this is that classical physics is not really deterministic: this is because, in general (ie. including chaotic systems), the evolution of a system depends on a set of initial conditions that are specified by full real numbers, impossible to measure with finite precision. So, the use of real numbers is hiding the indeterminism in the initial conditions, much like the function in this article encodes a dataset in a single parameter.
Basically, the universe can just as well be approximated in two different ways. One, it's all straight lines, and anything that looks like a circle/curve is actually a piece of a veeery many sided polygon if you look closely enough at it. Two, it's all curves of some curvature, and anything that looks like a straight line is actually a segment of a veeery large circle. The first perspective corresponds to taking the rational numbers as physical. The second one corresponds to taking pi as physical (and then it's unclear whether e is also physical, or which other transcendental numbers are, but 1 is definitely un-physical then).
Probably the constructive framework is the best way to express this concept, just starting from whatever constant we chose to define as the unit.
However, even if rarely used outside of proofs, they are the vast majority of the reals, in fact there are only countably infinite constructive/computable numbers.
i specifically said with a /discrete/ conception , geometry is infinitely dense (of discrete states)
Not to mention, the finer the distinctions between two states of a system, the more energy you need to distinguish them. So, the less impact these differences can have, unless the system is extraordinarily energetic (and even then, you end up in fundamental limits of energy per volume, like the Schwarzschild radius).
So again, there is no sense in which a finite part of the universe is universally dense.
Even worse for your argument, all currently known laws of physics use computable functions (the randomness in QM notwithstanding). So, by definition, all known laws of physics can be simulated by an ideal Turing machine (again, give or take some randomness in QM, depending on the interpretation you chose to believe in and on how you chose to simulate the QM system).
Also, by the same logic you apply to space, you could say that time is infinitely divisible, so you could create a computer which finishes an infinite amount of steps in a finite amount of time.