I’ve had this paper downloaded for about a decade and haven’t gotten around to reading it, but thinking about it, especially if space and time are quantized (an undetermined question last I checked and almost certainly still so), there would exist numbers in ℝ that cannot be expressed as physical quantities, even with an infinite universe. It’s possible that even the algebraic numbers include numbers that are non-physical (although it might be a larger subset of numbers than the constructible numbers depending on the structure of space-time’s quantization).
If reality is quantized and there is a smallest number that is physically relevant, you don't need the reals to break it. Take that smallest number and divide it by two, and now you have a physically meaningless number using only the rationals.
This isn't fair for what quantization means in reality, but I'm just pointing out that you don't have to introduce the real numbers to get physically meaningless quantities.
I think people overindex on the continuity problem with the reals. I'm personally a bit of real-number denier myself as a constructivist / intuitionalist.
But when we say things like "the rationals are discrete" or "the computable numbers are discrete" these are very specific claims in the domain of measure theory, a theory which yields almost nothing of value except endless paradoxes and naval-gazing nonsense. Similarly when people say "the rationals are countable" and "the computable numbers are countable" this is taking for granted the Cantor notion of measuring cardinality by bijective correspondence, once again, a theory that yields nothing of value except endless paradoxes and naval-gazing nonsense.
In the practical sense the rational numbers are quite continuous -- between any two rational numbers there are an infinite (unbounded) number of rational numbers -- there's no notion of a "leap" the way there is with the integers. And any useful number can be approximated arbitrarily closely by rationals.
And for computable numbers there's even less of a gap. With rationals you can only approximate. But you can have a computable number that is exactly equal to the square root of 2, because a computable number is the algorithm by which you form arbitrarily close approximations. The square of that computable number is itself computable and is exactly equal to 2.
What do "real" numbers buy you? That is, what do you get for the trouble of building your formalism around numbers that are not computable? Basically nothing.
And if you're worried that sticking to the rationals and the computable numbers is too much of a concession to "physical reality", rest assured -- the rationals are just as unphysical as the real numbers because they are continuous already, and physics does not give us the power to measure the difference between two sufficiently precise rational numbers just as it barfs when you throw "real" numbers at it.