Here's a low-tech way to look at it, which to me seems perfectly convincing.
Let C be some implementation of the reals via Cauchy sequences and D be some implementation of the reals via Dedekind cuts. Here C is "really" something like a tuple consisting of the set of reals, a relation corresponding to addition, etc.; D is a tuple with (allegedly) equivalent things implemented differently.
Let P(X) be the proposition that X is a tuple of the right size and that, when considered as an implementation of the real numbers, X satisfies the Birch-Swinnerton-Dyer conjecture. We have a proof -- perhaps a bizarre incomprehensible implementation-dependent one -- of P(C), in ZFC.
I claim that (again, in ZFC) P(C) iff P(D). Sketch of proof: 1. Up to canonical isomorphism there is only one complete ordered field. 2. C and D are complete ordered fields. 3. Therefore there is an isomorphism between C and D; in fact we can even write it down. 4. We can use this to build an isomorphism between C's complex numbers and D's complex numbers, and then between C's L-functions and D's L-functions, and C's elliptic curves and D's elliptic curves, and so on for every object required to state the BSD conjecture. 5. If we have a specific elliptic curve over D, these isomorphisms yield its equivalent over C (and vice versa); they pair up the groups of integer points in the two cases, showing that they have the same rank; they pair up the corresponding L-functions, showing that they have the same order of zero at s=1. 6. And we're done.
None of this requires that these isomorphisms be applied to the proof of P(C). That proof can be as C-specific as you like. What the isomorphisms show is that the things BSD says are equal come out the same way however you implement the real numbers.
How do we know that we can actually construct this pile of isomorphisms? By thinking about what objects we need in order to state the BSD conjecture, and how we build them, and noting that nothing in the process cares about "implementation details" of the real numbers. If you're sufficiently confident of your memory, you could do this "negatively" by noting that if when you were learning about elliptic curves and L-functions a lecturer had said something like "and of course this is true because the number 1 is just the same thing as the set containing just the empty set" you'd have noticed and been horrified. Otherwise, you can (tediously but straightforwardly) go through the usual textbooks and check that the constructions are all "sane".