1. One-way functions are not all cryptography. Some constructions may need stronger assumptions than one-way functions (we don't know yet if they do). So this problem is a “Master Problem” only for a subset of cryptography (symmetric encryption, pseudorandom generators, etc.).
2. This is not the first “Master Problem” to base one-way functions on. There's Levin's complete one way function [1; Section 4.3]. Breaking it is proven to be as hard as any other one-way function, in other words if there exist one-way functions then this is one of them. But Levin's construction is somewhat artificial (it combines many one-way function candidates to create the “master one-way function”) and is not as surprising since its techniques and formulation are similar to how the usual one-way functions are defined. The connection from the linked article, on the other hand, is very surprising and unusual; it connects one-way functions to a more distant field which (to me) seems to be operating with quite different concepts.
It's also fun to know that similar “Master Problems” exist for other primitives too. For example, for public-key encryption there's a Complete Public Key cryptosystem [2]. Albeit this one is similar in spirit to Levin's construction (not as surprising IMO as the linked article), the complete cryptosystem is obtained by combining many other cryptosystems.
[1]: https://arxiv.org/abs/cs/0012023
[2]: https://eccc.weizmann.ac.il//eccc-reports/2006/TR06-046/inde...