If you were writing software for something intended to traverse the Interplanetary transfer network then you would probably use charts and atlases and transition functions, and you would study (symplectic) manifolds and homeomorphisms in order to understand those more-applied concepts.
If an otherwise useful theorem assumes that the manifold is orientable, then you need to show that your practical manifold is orientable before you can use it—and if it turns out not to be orientable, then you can’t use it at all. If instead you had an analogous theorem that applied to all manifolds, then you could use it immediately.
I understand your point—it’s akin to the Box quote “all models are wrong but some are useful”—when choosing among (false) models, choose the most useful one. However, it is not the case that stronger assumptions are more useful—of course stronger assumptions make the task of proving easier, but the task as a whole includes both proving and also building a system based on the theorems proven.
My primary point is that EY is implying that second-order logic is necessary to work with the integers. People work with the integers without using second-order logic all the time. If he said that he is only introducing second-order logic for convenience in proving and there are certainly other ways of doing it, and that some people (intuitionists and finitists) think that introducing second-order logic is a dubious move, I’d be happy.
My other claim that second-order logic is unphysical and that its unphysicality probably does ripple out to make practical tasks more difficult, is a secondary one. I’m happy to agree that this secondary claim is not mainstream.