It seems to me like this discussion has gotten too far into either/or "winning". The prevalance of encodings in mathematics and logic (e.g. encoding the concept of pairing in set theory by defining (a, b) to be the set {{a}, {a, b}}, the double negation encoding of classical logic inside intuitionist logic, et cetera) means that the things we point to as "foundations" such as the ZF axioms for set theory are not actually foundational, in the sense of necessary and supporting. ZF is one possible system which is sufficiently strong to encode the things that we want to do. There are many other systems which are also sufficiently strong, and getting multiple perspectives on a topic by starting from different alternative "foundations" is probably a good thing. You do not have to choose just one!
Another way to look at it is - the things that we call foundations of mathematics are like the Planck length - yes, according to our current best theory, that's the smallest, most basic element. However, that doesn't mean it is stable; rather, it's cutting edge (admittedly, Planck length is more at the cutting edge of physics than foundations of mathematics are at a cutting edge of mathematics). The stable things are more like cubits and inches - central, human-scale "theorems" such that if a new alternative foundation of mathematics contradicted them, we would throw away the foundation rather than the theorem. Some candidate "cubit" or "inch" theorems (really, arguments) might be the infinitude of primes, or the irrationality of the square root of 2.
Friedman and Simpson have a program of "Reverse Mathematics", studying in what way facts that we normally think of as theorems, like the Heine-Borel theorem, pin down things that we normally think of as logic axioms, such as induction schemas. I really think that Simpson's paper "Partial Realizations of Hilbert's Program" is insightful and helpful to this discussion: http://www.math.psu.edu/simpson/papers/hilbert.ps
Lakatos's "Proofs and Refutations" is also helpful, explaining in what sense a flawed and/or informal argument is helpful - Note that Lakatos calls arguments proofs, even when they're flawed and/or informal, implicitly suggesting that everyone calls their arguments proofs until the flaws are pointed out. I understand he retreated from that philosophical position later in life, but that pre-retreat philosophical position might still be tenable.
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Ok, right. I think I didn't fully appreciate your point before. So the fact that a particular many-sorted first-order logic with extra axioms is proof-theoretically equivalent to (a given proof system for) 2nd-order logic should make me stop asking whether we should build machines with one or the other, and start asking instead whether the many-sorted logic with extra axioms is any better than plain first-order logic (to which the answer appears to be yes, based on our admittedly 2nd-order reasoning). Right?
The prevalence of encodings means that we might not be able to "build machines with one or the other". That is, given that there are basic alternatives A and B and A can encode B and B can encode A, it would take a technologist specializing in hair-splitting to say whether a machine that purportedly is using A is "really" using A at its lowest level or whether it is "actually" using B and only seems to use A via an encoding.
If in the immediate term you want to work with many-sorted first order logic, a reasonable first step would be to implement single-sorted first order logic, and a preprocessor to translate the many-sorted syntax into the single-sorted syntax. Then further development, optimizations and so on, might complicate the story, compacting the preprocessor and single-sorted engine into a single technology that you might reasonably say implements many-sorted logic "natively".
The prevalence of encodings means that apparently different foundations don't always make a difference.