In fact, part of the appeal I find in rational trigonometry is that it should be easier to adapt for computing, since as you pointed out, computers can not represent irrational numbers. Yet trigonometric functions usually return irrational numbers, and a computer can't do better than approximate them.
On the contrary, it is possible to do exact arithmetic on rational numbers. Granted, you can't do that with floating points, though.
PS. To be clear: although the numbers actually used in the code are floating point numbers, the equations have a purely algebraic form (no sine, cosine or sqrt), so it should at least in principle be possible to use a Rational number type instead, and the computation would then be exact. The only approximation would be due to the Runge-Kutta algorithm.