The top-down (mathematical) approach can also fail, in cases where there's not an existing math solution, or when a perfectly spherical cow isn't an adequate representation of reality. See Minix vs Linux, or OSI vs TCP/IP.
But I think the Sudoku example is less about top-down vs bottom-up and more about dogmatic adherence to abstractions (OOP in that case). Jeffries wasn't just using a 'hacker' approach - he was forcing everything through an OOP lens that fundamentally didn't fit the problem structure.
But yes, same issue can happen with the 'mathematical' approach - forcing "elegant" closed-form thinking onto problems that are inherently messy or iterative.
IMO, the mathematical approach is essentially always better for software; nearly every problem that the industry didn’t inflict upon itself was solved by some egghead last century. But there is a kind of joy in creating pointless difficulties at enormous cost in order to experience the satisfaction of overcoming them without recourse to others, I suppose.