Pi is a concept that is divorced from reality, Pi is irrational because a chain of logical inferences and applications result in the definition. The definition of Pi is predicated on a geometric description of a circle which is distinctly non-physical. The entire meaning of Pi is based on a logical chain of defined symbols, that while meaningful to some conscious thinker are not observations of physical reality. The geometric conception of a circle as an infinite collection of points, which are inherently not physically possible objects, exhibits a ratio between its radius and its diameter, which is called Pi, and that ratio needs to be expressed by a number which is definitionally irrational (the definition of which is predicated on a definition of Natural numbers (via a definition of the Real numbers)). These symbols are merely the language we use to describe logical relations between various symbols, that while possibly applicable, with prediction and accuracy preconditions, to physical reality, are merely a logic used to describe natural numbers and the properties thereof.
It is this complete logical decoupling from any physical, observable reality, that I cannot accept mathematics as anything other than an, ideally, internally consistent, logic used to define and discuss symbolic logical objects. And I am of the opinion that logics are merely invented by conscious beings as means to systematize areas of discourse and to derive internally consistent inferences and implications built there on.
I would agree that if irrational numbers were prohibited from being inferred in the logical system of math then some things would not work within the logic. Because a change in the axiomatic or inferential rules of a logic are changed the logic as a whole changes. But, if, as you describe it, math was forked to be limited to rationals, and the precision of those radicals was calibrated to be on the order of 1/10 of a Planck length, I am not convinced that any equation attempting to describe 3 dimensional space would be inaccurate. However, I could wrong.