What is the relationship between the molecular weight of a polymer and that of polystyrene?
You have to have something to calibrate the column with. Polystyrene is typically used since it can be made cheaply (well, relatively cheaply) with a pretty small molecular weight distribution.

Yes, there will be differences between the true molecular weight of a polymer and what the comparison to polystyrene gives you. But does that really matter? Why do you need to know the absolute molecular weight, when a relative comparison works just fine?

It's similar to how we determine the mass of something. At present, there is that infamous block of Pt/Ir in Paris that is the standard kilogram. All mass measurements are made through a series of comparison to that mass.